1
|
Dodin A, Geissler PL. Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics. J Chem Theory Comput 2023; 19:2906-2917. [PMID: 37130215 DOI: 10.1021/acs.jctc.3c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. We show that existing force fields that place all non-Coulomb forces on the Drude core and none on the shell inadvertently couple the dipole to non-Coulombic forces. This introduces errors where interactions with neutral particles can erroneously induce atomic polarization, leading to spurious polarizations in the absence of an electric field, exacerbating violations of equipartition in the employed Carr-Parinello scheme. A suitable symmetrization of the interaction potential that correctly splits the force between the Drude core and shell can correct this shortcoming, improving the stability and numerical performance of Drude oscillator-based simulations. The symmetrization procedure is straightforward and only requires the rescaling of a few force field parameters.
Collapse
Affiliation(s)
- Amro Dodin
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
2
|
Rogers JR, Geissler PL. Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts. PLoS Comput Biol 2023; 19:e1010992. [PMID: 37036851 PMCID: PMC10085062 DOI: 10.1371/journal.pcbi.1010992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Cellular distributions of the sphingolipid ceramide-1-phosphate (C1P) impact essential biological processes. C1P levels are spatiotemporally regulated by ceramide-1-phosphate transfer protein (CPTP), which efficiently shuttles C1P between organelle membranes. Yet, how CPTP rapidly extracts and inserts C1P into a membrane remains unknown. Here, we devise a multiscale simulation approach to elucidate biophysical details of CPTP-mediated C1P transport. We find that CPTP binds a membrane poised to extract and insert C1P and that membrane binding promotes conformational changes in CPTP that facilitate C1P uptake and release. By significantly disrupting a lipid's local hydrophobic environment in the membrane, CPTP lowers the activation free energy barrier for passive C1P desorption and enhances C1P extraction from the membrane. Upon uptake of C1P, further conformational changes may aid membrane unbinding in a manner reminiscent of the electrostatic switching mechanism used by other lipid transfer proteins. Insertion of C1P into an acceptor membrane, eased by a decrease in membrane order by CPTP, restarts the transfer cycle. Most notably, we provide molecular evidence for CPTP's ability to catalyze C1P extraction by breaking hydrophobic C1P-membrane contacts with compensatory hydrophobic lipid-protein contacts. Our work, thus, provides biophysical insights into how CPTP efficiently traffics C1P between membranes to maintain sphingolipid homeostasis and, additionally, presents a simulation method aptly suited for uncovering the catalytic mechanisms of other lipid transfer proteins.
Collapse
Affiliation(s)
- Julia R Rogers
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| |
Collapse
|
3
|
Omar AK, Klymko K, GrandPre T, Geissler PL, Brady JF. Tuning nonequilibrium phase transitions with inertia. J Chem Phys 2023; 158:074904. [PMID: 36813709 DOI: 10.1063/5.0138256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In striking contrast to equilibrium systems, inertia can profoundly alter the structure of active systems. Here, we demonstrate that driven systems can exhibit effective equilibrium-like states with increasing particle inertia, despite rigorously violating the fluctuation-dissipation theorem. Increasing inertia progressively eliminates motility-induced phase separation and restores equilibrium crystallization for active Brownian spheres. This effect appears to be general for a wide class of active systems, including those driven by deterministic time-dependent external fields, whose nonequilibrium patterns ultimately disappear with increasing inertia. The path to this effective equilibrium limit can be complex, with finite inertia sometimes acting to accentuate nonequilibrium transitions. The restoration of near equilibrium statistics can be understood through the conversion of active momentum sources to passive-like stresses. Unlike truly equilibrium systems, the effective temperature is now density dependent, the only remnant of the nonequilibrium dynamics. This density-dependent temperature can in principle introduce departures from equilibrium expectations, particularly in response to strong gradients. Our results provide additional insight into the effective temperature ansatz while revealing a mechanism to tune nonequilibrium phase transitions.
Collapse
Affiliation(s)
- Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | - Katherine Klymko
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Trevor GrandPre
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
4
|
Hamerlynck LM, Bischoff AJ, Rogers JR, Roberts TD, Dai J, Geissler PL, Francis MB, Ginsberg NS. Static Disorder has Dynamic Impact on Energy Transport in Biomimetic Light-Harvesting Complexes. J Phys Chem B 2022; 126:7981-7991. [PMID: 36191182 PMCID: PMC9574921 DOI: 10.1021/acs.jpcb.2c06614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Despite extensive studies, many questions remain about
what structural
and energetic factors give rise to the remarkable energy transport
efficiency of photosynthetic light-harvesting protein complexes, owing
largely to the inability to synthetically control such factors in
these natural systems. Herein, we demonstrate energy transfer within
a biomimetic light-harvesting complex consisting of identical chromophores
attached in a circular array to a protein scaffold derived from the
tobacco mosaic virus coat protein. We confirm the capability of energy
transport by observing ultrafast depolarization in transient absorption
anisotropy measurements and a redshift in time-resolved emission spectra
in these complexes. Modeling the system with kinetic Monte Carlo simulations
recapitulates the observed anisotropy decays, suggesting an inter-site
hopping rate as high as 1.6 ps–1. With these simulations,
we identify static disorder in orientation, site energy, and degree
of coupling as key remaining factors to control to achieve long-range
energy transfer in these systems. We thereby establish this system
as a highly promising, bottom-up model for studying long-range energy
transfer in light-harvesting protein complexes.
Collapse
Affiliation(s)
- Leo M Hamerlynck
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Amanda J Bischoff
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Julia R Rogers
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Trevor D Roberts
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Jing Dai
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States
| | - Phillip L Geissler
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Naomi S Ginsberg
- Department of Chemistry, University of California Berkeley, Berkeley, California94720, United States.,Department of Physics, University of California Berkeley, Berkeley, California94720, United States.,Kavli Energy NanoSciences Institute, Berkeley, California94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| |
Collapse
|
5
|
Wrona PR, Rabani E, Geissler PL. A Pair of 2D Quantum Liquids: Investigating the Phase Behavior of Indirect Excitons. ACS Nano 2022; 16:15339-15346. [PMID: 36069715 PMCID: PMC9527805 DOI: 10.1021/acsnano.2c06947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Long-lived indirect excitons (IXs) exhibit a rich phase diagram, including a Bose-Einstein condensate (BEC), a Wigner crystal, and other exotic phases. Recent experiments have hinted at a "classical" liquid of IXs above the BEC transition. To uncover the nature of this phase, we use a broad range of theoretical tools and find no evidence of a driving force toward classical condensation. Instead, we attribute the condensed phase to a quantum electron-hole liquid (EHL), first proposed by Keldysh for direct excitons. Taking into account the association of free carriers into bound excitons, we study the phase equilibrium between a gas of excitons, a gas of free carriers, and an EHL for a wide range of electron-hole separations, temperatures, densities, and mass ratios. Our results agree reasonably well with recent measurements of GaAs/AlGaAs coupled quantum wells.
Collapse
Affiliation(s)
- Paul R. Wrona
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Eran Rabani
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- The
Raymond and Beverly Sackler Center of Computational Molecular and
Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Phillip L. Geissler
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
6
|
Abstract
Experiments and computer simulations have established that liquid water's surfaces can deviate in important ways from familiar bulk behavior. Even in the simplest case of an air-water interface, distinctive layering, orientational biases, and hydrogen bond arrangements have been reported, but an overarching picture of their origins and relationships has been incomplete. Here we show that a broad set of such observations can be understood through an analogy with the basal face of crystalline ice. Using simulations, we demonstrate a number of structural similarities between water and ice surfaces, suggesting the presence of domains at the air-water interface with ice-like features that persist over 2-3 molecular diameters. Most prominent is a shared characteristic layering of molecular density and orientation perpendicular to the interface. Lateral correlations of hydrogen bond network geometry point to structural similarities in the parallel direction as well. Our results bolster and significantly extend previous conceptions of ice-like structure at the liquid's boundary and suggest that the much-discussed quasi-liquid layer on ice evolves subtly above the melting point into a quasi-ice layer at the surface of liquid water.
Collapse
Affiliation(s)
- Nathan L Odendahl
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
7
|
Ondry JC, Frechette LB, Geissler PL, Alivisatos AP. Trade-offs between Translational and Orientational Order in 2D Superlattices of Polygonal Nanocrystals with Differing Edge Count. Nano Lett 2022; 22:389-395. [PMID: 34935383 DOI: 10.1021/acs.nanolett.1c04058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The goal of this work is to identify factors which modulate structural order in 2D self-assembled superlattices of polygon-shaped colloidal nanocrystals. Using combined experimental and simulation techniques, we quantify order in superlattices of hexagonal prism-shaped CdSe/CdS nanocrystals and cube-shaped CsPbBr3 nanocrystals. Superlattices derived from cube-shaped nanocrystals display less translational order compared to hexagonal prism-shaped nanocrystals both experimentally and in simulations. This effect can be attributed to geometric considerations inherent to the combined rotational and translational symmetries of different polygonal shapes and their superlattices. Cubes form a simple cubic lattice where nanocrystals can slide without steric overlap, whereas hexagonal prisms interlock, preventing translation. Regarding orientational order, cube assemblies display a narrower orientation distribution. Intuitively, hexagonal prisms are a more "spherical" shape compared to cubes. The results presented here outline a conceptual framework for identifying superlattice structures which favor translationally and orientationally ordered self-assembled superlattices.
Collapse
Affiliation(s)
- Justin C Ondry
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, Berkeley, California 94720, United States
| | - Layne B Frechette
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - A Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
8
|
Abstract
The surface of a polar liquid presents a special environment for the solvation and organization of charged solutes, which differ from bulk behaviors in important ways. These differences have motivated many attempts to understand electrostatic response at aqueous interfaces in terms of a spatially varying dielectric permittivity, typically concluding that the dielectric constant of interfacial water is significantly lower than in the bulk liquid. Such analyses, however, are complicated by the potentially nonlocal nature of dielectric response over the short length scales of interfacial heterogeneity. Here we circumvent this problem for thin water films by adopting a thermodynamic approach. Using molecular simulations, we calculate the solvent's contribution to the reversible work of charging a parallel plate capacitor. We find good agreement with a simple dielectric continuum model that assumes bulk dielectric permittivity all the way up to the liquid's boundary, even for very thin (∼1 nm) films. This comparison requires careful attention to the placement of dielectric boundaries between liquid and vapor, which also resolves apparent discrepancies with dielectric imaging experiments. Free energy calculations from molecular simulations reveal that water's interfacial dielectric response is well-described by bulk properties.![]()
Collapse
Affiliation(s)
- Stephen J. Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Phillip L. Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
9
|
Abstract
We study the initial stages of homogeneous melting of a hexagonal ice crystal at coexistence and at moderate superheating. Our trajectory-based computer simulation approach provides a comprehensive picture of the events that lead to melting, from the initial accumulation of 5+7 defects, via the formation of L-D and interstitial-vacancy pairs, to the formation of a liquid nucleus. Of the different types of defects that we observe to be involved in melting, a particular kind of 5+7 type defect (type 5) plays a prominent role as it often forms prior to the formation of the initial liquid nucleus and close to the site where the nucleus forms. Hence, like other solids, ice homogeneously melts via the prior accumulation of defects.
Collapse
Affiliation(s)
- Clemens Moritz
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| |
Collapse
|
10
|
Forth J, Mariano A, Chai Y, Toor A, Hasnain J, Jiang Y, Feng W, Liu X, Geissler PL, Menon N, Helms BA, Ashby PD, Russell TP. The Buckling Spectra of Nanoparticle Surfactant Assemblies. Nano Lett 2021; 21:7116-7122. [PMID: 34448588 DOI: 10.1021/acs.nanolett.1c01454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fine control over the mechanical properties of thin sheets underpins transcytosis, cell shape, and morphogenesis. Applying these principles to artificial, liquid-based systems has led to reconfigurable materials for soft robotics, actuation, and chemical synthesis. However, progress is limited by a lack of synthetic two-dimensional membranes that exhibit tunable mechanical properties over a comparable range to that seen in nature. Here, we show that the bending modulus, B, of thin assemblies of nanoparticle surfactants (NPSs) at the oil-water interface can be varied continuously from sub-kBT to 106kBT, by varying the ligands and particles that comprise the NPS. We find extensive departure from continuum behavior, including enormous mechanical anisotropy and a power law relation between B and the buckling spectrum width. Our findings provide a platform for shape-changing liquid devices and motivate new theories for the description of thin-film wrinkling.
Collapse
Affiliation(s)
- Joe Forth
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University College London, London, WC1H 0AJ, United Kingdom
| | - Andres Mariano
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yu Chai
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China
| | - Anju Toor
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- School of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Jaffar Hasnain
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yufeng Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- School of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Wenqian Feng
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xubo Liu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Phillip L Geissler
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Narayanan Menon
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Brett A Helms
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul D Ashby
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thomas P Russell
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Polymer Science and Engineering Department, University of Massachusetts, 120 Governors Drive, Conte Center for Polymer Research, Amherst, Massachusetts 01003, United States
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| |
Collapse
|
11
|
Rogers JR, Espinoza Garcia G, Geissler PL. Membrane hydrophobicity determines the activation free energy of passive lipid transport. Biophys J 2021; 120:3718-3731. [PMID: 34302793 PMCID: PMC8456290 DOI: 10.1016/j.bpj.2021.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/07/2021] [Accepted: 07/19/2021] [Indexed: 12/16/2022] Open
Abstract
The collective behavior of lipids with diverse chemical and physical features determines a membrane's thermodynamic properties. Yet, the influence of lipid physicochemical properties on lipid dynamics, in particular interbilayer transport, remains underexplored. Here, we systematically investigate how the activation free energy of passive lipid transport depends on lipid chemistry and membrane phase. Through all-atom molecular dynamics simulations of 11 chemically distinct glycerophospholipids, we determine how lipid acyl chain length, unsaturation, and headgroup influence the free energy barriers for two elementary steps of lipid transport: lipid desorption, which is rate limiting, and lipid insertion into a membrane. Consistent with previous experimental measurements, we find that lipids with longer, saturated acyl chains have increased activation free energies compared to lipids with shorter, unsaturated chains. Lipids with different headgroups exhibit a range of activation free energies; however, no clear trend based solely on chemical structure can be identified, mirroring difficulties in the interpretation of previous experimental results. Compared to liquid-crystalline phase membranes, gel phase membranes exhibit substantially increased free energy barriers. Overall, we find that the activation free energy depends on a lipid's local hydrophobic environment in a membrane and that the free energy barrier for lipid insertion depends on a membrane's interfacial hydrophobicity. Both of these properties can be altered through changes in lipid acyl chain length, lipid headgroup, and membrane phase. Thus, the rate of lipid transport can be tuned through subtle changes in local membrane composition and order, suggesting an unappreciated role for nanoscale membrane domains in regulating cellular lipid dynamics.
Collapse
Affiliation(s)
- Julia R Rogers
- Department of Chemistry, University of California Berkeley, Berkeley, California.
| | | | - Phillip L Geissler
- Department of Chemistry, University of California Berkeley, Berkeley, California; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California.
| |
Collapse
|
12
|
Ahmed M, Blum M, Crumlin EJ, Geissler PL, Head-Gordon T, Limmer DT, Mandadapu KK, Saykally RJ, Wilson KR. Molecular Properties and Chemical Transformations Near Interfaces. J Phys Chem B 2021; 125:9037-9051. [PMID: 34365795 DOI: 10.1021/acs.jpcb.1c03756] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The properties of bulk water and aqueous solutions are known to change in the vicinity of an interface and/or in a confined environment, including the thermodynamics of ion selectivity at interfaces, transition states and pathways of chemical reactions, and nucleation events and phase growth. Here we describe joint progress in identifying unifying concepts about how air, liquid, and solid interfaces can alter molecular properties and chemical reactivity compared to bulk water and multicomponent solutions. We also discuss progress made in interfacial chemistry through advancements in new theory, molecular simulation, and experiments.
Collapse
Affiliation(s)
- Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Monika Blum
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ethan J Crumlin
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David T Limmer
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kranthi K Mandadapu
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Richard J Saykally
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin R Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
13
|
Cox SJ, Mandadapu KK, Geissler PL. Quadrupole-mediated dielectric response and the charge-asymmetric solvation of ions in water. J Chem Phys 2021; 154:244502. [PMID: 34241373 DOI: 10.1063/5.0051399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of the solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for basic length and energy scales of ion solvation, computer simulations indicate not only its quantitative inaccuracies but also its inability to capture some basic and important aspects of microscopic polarization response. Here, we consider one such shortcoming, a failure to distinguish the solvation thermodynamics of cations from that of otherwise-identical anions, and we pursue a simple, physically inspired modification of the dielectric continuum model to address it. The adaptation is motivated by analyzing the orientational response of an isolated water molecule whose dipole is rigidly constrained. Its free energy suggests a Hamiltonian for dipole fluctuations that accounts implicitly for the influence of higher-order multipole moments while respecting constraints of molecular geometry. We propose a field theory with the suggested form, whose nonlinear response breaks the charge symmetry of ion solvation. An approximate variational solution of this theory, with a single adjustable parameter, yields solvation free energies that agree closely with simulation results over a considerable range of solute size and charge.
Collapse
Affiliation(s)
- Stephen J Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kranthi K Mandadapu
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
14
|
Omar AK, Klymko K, GrandPre T, Geissler PL. Phase Diagram of Active Brownian Spheres: Crystallization and the Metastability of Motility-Induced Phase Separation. Phys Rev Lett 2021; 126:188002. [PMID: 34018789 DOI: 10.1103/physrevlett.126.188002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/06/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Motility-induced phase separation (MIPS), the phenomenon in which purely repulsive active particles undergo a liquid-gas phase separation, is among the simplest and most widely studied examples of a nonequilibrium phase transition. Here, we show that states of MIPS coexistence are in fact only metastable for three-dimensional active Brownian particles over a very broad range of conditions, decaying at long times through an ordering transition we call active crystallization. At an activity just above the MIPS critical point, the liquid-gas binodal is superseded by the crystal-fluid coexistence curve, with solid, liquid, and gas all coexisting at the triple point where the two curves intersect. Nucleating an active crystal from a disordered fluid, however, requires a rare fluctuation that exhibits the nearly close-packed density of the solid phase. The corresponding barrier to crystallization is surmountable on a feasible timescale only at high activity, and only at fluid densities near maximal packing. The glassiness expected for such dense liquids at equilibrium is strongly mitigated by active forces, so that the lifetime of liquid-gas coexistence declines steadily with increasing activity, manifesting in simulations as a facile spontaneous crystallization at extremely high activity.
Collapse
Affiliation(s)
- Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Katherine Klymko
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Trevor GrandPre
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
15
|
Hasnain J, Jiang Y, Hou H, Yan J, Athanasopoulou L, Forth J, Ashby PD, Helms BA, Russell TP, Geissler PL. Spontaneous emulsification induced by nanoparticle surfactants. J Chem Phys 2020; 153:224705. [PMID: 33317311 DOI: 10.1063/5.0029016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Microemulsions, mixtures of oil, water, and surfactant, are thermodynamically stable. Unlike conventional emulsions, microemulsions form spontaneously, have a monodisperse droplet size that can be controlled by adjusting the surfactant concentration, and do not degrade with time. To make microemulsions, a judicious choice of surfactant molecules must be made, which significantly limits their potential use. Nanoparticle surfactants, on the other hand, are a promising alternative because the surface chemistry needed to make them bind to a liquid-liquid interface is both well flexible and understood. Here, we derive a thermodynamic model predicting the conditions in which nanoparticle surfactants drive spontaneous emulsification that agrees quantitatively with experiments using Noria nanoparticles. This new class of microemulsions inherits the mechanical, chemical, and optical properties of the nanoparticles used to form them, leading to novel applications.
Collapse
Affiliation(s)
- J Hasnain
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Y Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - H Hou
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - J Yan
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L Athanasopoulou
- Faculty of Mathematics and Physics, University of Ljubjana, Jadranska 19, SI-1000 Ljubjana, Slovenia
| | - J Forth
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - P D Ashby
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - B A Helms
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - T P Russell
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - P L Geissler
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, USA
| |
Collapse
|
16
|
Moritz C, Sega M, Innerbichler M, Geissler PL, Dellago C. Weak scaling of the contact distance between two fluctuating interfaces with system size. Phys Rev E 2020; 102:062801. [PMID: 33465946 DOI: 10.1103/physreve.102.062801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
A pair of flat parallel surfaces, each freely diffusing along the direction of their separation, will eventually come into contact. If the shapes of these surfaces also fluctuate, then contact will occur when their centers-of-mass remain separated by a nonzero distance ℓ. An example of such a situation is the motion of interfaces between two phases at conditions of thermodynamic coexistence, and in particular the annihilation of domain wall pairs under periodic boundary conditions. Here we present a general approach to calculate the probability distribution of the contact distance ℓ and determine how its most likely value ℓ^{*} depends on the surfaces' lateral size L. Using the Edward-Wilkinson equation as a model for interfaces, we demonstrate that ℓ^{*} scales weakly with system size, i.e., the dependence of ℓ^{*} on L for both (1+1)- and (2+1)-dimensional interfaces is such that lim_{L→∞}(ℓ^{*}/L)=0. In particular, for (2+1)-dimensional interfaces ℓ^{*} is an algebraic function of logL, a result that is confirmed by computer simulations of slab-shaped domains formed under periodic boundary conditions. This weak scaling implies that such domains remain topologically intact until ℓ becomes very small compared to the lateral size of the interface, contradicting expectations from equilibrium thermodynamics.
Collapse
Affiliation(s)
- Clemens Moritz
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Marcello Sega
- Forschungszentrum Jülich GmbH, Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Fürther Straße 248, 90429 Nürnberg, Germany
| | - Max Innerbichler
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Erwin Schrödinger Institute for Mathematics and Physics, Boltzmanngasse 9, 1090, Vienna, Austria
| |
Collapse
|
17
|
Cox SJ, Thorpe DG, Shaffer PR, Geissler PL. Assessing long-range contributions to the charge asymmetry of ion adsorption at the air-water interface. Chem Sci 2020; 11:11791-11800. [PMID: 34094413 PMCID: PMC8162909 DOI: 10.1039/d0sc01947j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Anions generally associate more favorably with the air–water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this bias. Here we assess quantitatively the role that intrinsic charge asymmetry of water's surface plays in ion adsorption, using computer simulations to compare model solutes of various size and charge. In doing so, we also evaluate the degree to which linear response theory for solvent polarization is a reasonable approach for comparing the thermodynamics of bulk and interfacial ion solvation. Consistent with previous works on bulk ion solvation, we find that the average electrostatic potential at the center of a neutral, sub-nanometer solute at the air–water interface depends sensitively on its radius, and that this potential changes quite nonlinearly as the solute's charge is introduced. The nonlinear response closely resembles that of the bulk. As a result, the net nonlinearity of ion adsorption is weaker than in bulk, but still substantial, comparable to the apparent magnitude of macroscopically nonlocal contributions from the undisturbed interface. For the simple-point-charge model of water we study, these results argue distinctly against rationalizing ion adsorption in terms of surface potentials inherent to molecular structure of the liquid's boundary. Cations and anions have different affinities for the air-water interface. The intrinsic orientation of surface molecules suggests such an asymmetry, but the bias is dominated by solvent response that is spatially local and significantly nonlinear.![]()
Collapse
Affiliation(s)
- Stephen J Cox
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Dayton G Thorpe
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Physics, University of California Berkeley CA 94720 USA
| | - Patrick R Shaffer
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Chemistry, University of California Berkeley CA 94720 USA
| |
Collapse
|
18
|
Affiliation(s)
- Julia R. Rogers
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
19
|
Mizuno H, Oosterbaan KJ, Menzl G, Smith J, Rizzuto AM, Geissler PL, Head-Gordon M, Saykally RJ. Revisiting the π → π* transition of the nitrite ion at the air/water interface: A combined experimental and theoretical study. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
20
|
Rogers JR, Geissler PL. Transition States of Passive Lipid Transport are Characterized by Hydrophobic Contacts. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
21
|
Frechette LB, Dellago C, Geissler PL. Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids. Phys Rev Lett 2019; 123:135701. [PMID: 31697506 DOI: 10.1103/physrevlett.123.135701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Lattice mismatch can substantially impact the spatial organization of heterogeneous materials. We examine a simple model for lattice-mismatched solids over a broad range of temperature and composition, revealing both uniform and spatially modulated phases. Scenarios for coexistence among them are unconventional due to the extensive mechanical cost of segregation. Together with an adapted Maxwell construction for elastic phase separation, mean field theory predicts a phase diagram that captures key low-temperature features of Monte Carlo simulations.
Collapse
Affiliation(s)
- Layne B Frechette
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Erwin Schrödinger Institute for Mathematics and Physics, University of Vienna, Boltzmanngasse 9, Wien 1090, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Wien 1090, Austria and Erwin Schrödinger Institute for Mathematics and Physics, University of Vienna, Boltzmanngasse 9, Wien 1090, Austria
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Erwin Schrödinger Institute for Mathematics and Physics, University of Vienna, Boltzmanngasse 9, Wien 1090, Austria
| |
Collapse
|
22
|
Affiliation(s)
- Stephen J. Cox
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Phillip L. Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
23
|
Delor M, Dai J, Roberts TD, Rogers JR, Hamed SM, Neaton JB, Geissler PL, Francis MB, Ginsberg NS. Exploiting Chromophore–Protein Interactions through Linker Engineering To Tune Photoinduced Dynamics in a Biomimetic Light-Harvesting Platform. J Am Chem Soc 2018; 140:6278-6287. [DOI: 10.1021/jacs.7b13598] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Jeffrey B. Neaton
- Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
| | | | | | - Naomi S. Ginsberg
- Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
| |
Collapse
|
24
|
Garrahan JP, Geissler PL, Limmer DT. Virtual Issue in Memory of David Chandler. J Phys Chem B 2018; 121:5309-5311. [PMID: 28565909 DOI: 10.1021/acs.jpcb.7b04830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Phillip L Geissler
- University of California, Berkeley.,Lawrence Berkeley National Laboratory
| | - David T Limmer
- University of California, Berkeley.,Kavli Energy NanoScience Institute.,Lawrence Berkeley National Laboratory
| |
Collapse
|
25
|
Forth J, Liu X, Hasnain J, Toor A, Miszta K, Shi S, Geissler PL, Emrick T, Helms BA, Russell TP. Reconfigurable Printed Liquids. Adv Mater 2018; 30:e1707603. [PMID: 29573293 DOI: 10.1002/adma.201707603] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Liquids lack the spatial order required for advanced functionality. Interfacial assemblies of colloids, however, can be used to shape liquids into complex, 3D objects, simultaneously forming 2D layers with novel magnetic, plasmonic, or structural properties. Fully exploiting all-liquid systems that are structured by their interfaces would create a new class of biomimetic, reconfigurable, and responsive materials. Here, printed constructs of water in oil are presented. Both form and function are given to the system by the assembly and jamming of nanoparticle surfactants, formed from the interfacial interaction of nanoparticles and amphiphilic polymers that bear complementary functional groups. These yield dissipative constructs that exhibit a compartmentalized response to chemical cues. Potential applications include biphasic reaction vessels, liquid electronics, novel media for the encapsulation of cells and active matter, and dynamic constructs that both alter, and are altered by, their external environment.
Collapse
Affiliation(s)
- Joe Forth
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Xubo Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jaffar Hasnain
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Anju Toor
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Mechanical Engineering, University of California, Berkeley, CA, 94720, USA
| | - Karol Miszta
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Shaowei Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Todd Emrick
- Polymer Science and Engineering Department, Conte Center for Polymer Research, University of Massachusetts, 120 Governors Drive, Amherst, MA, 01003, USA
| | - Brett A Helms
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas P Russell
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, Beijing University of Chemical Technology, Beijing, 100029, China
- Polymer Science and Engineering Department, Conte Center for Polymer Research, University of Massachusetts, 120 Governors Drive, Amherst, MA, 01003, USA
- WPI - Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba, Sendai, 980-8577, Japan
| |
Collapse
|
26
|
DuBay KH, Iwan K, Osorio-Planes L, Geissler PL, Groll M, Trauner D, Broichhagen J. A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity. ACS Chem Biol 2018; 13:793-800. [PMID: 29357237 DOI: 10.1021/acschembio.7b00862] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Optogenetics and photopharmacology are powerful approaches to investigating biochemical systems. While the former is based on genetically encoded photoreceptors that utilize abundant chromophores, the latter relies on synthetic photoswitches that are either freely diffusible or covalently attached to specific bioconjugation sites, which are often native or engineered cysteines. The identification of suitable cysteine sites and appropriate linkers for attachment is generally a lengthy and cumbersome process. Herein, we describe an in silico screening approach that is designed to propose a small number of optimal combinations. By applying this computational approach to human carbonic anhydrase and a set of three photochromic tethered ligands, the number of potential site-ligand combinations was narrowed from over 750 down to 6, which we then evaluated experimentally. Two of these six combinations resulted in light-responsive human Carbonic Anhydrases (LihCAs), which were characterized with enzymatic activity assays, mass spectrometry, and X-ray crystallography. Our study also provides insights into the reactivity of cysteines toward maleimides and the hydrolytic stability of the adducts obtained.
Collapse
Affiliation(s)
- Kateri H. DuBay
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Katharina Iwan
- Department of Chemistry, Ludwig-Maximilian-University Munich and Munich Center for Integrated Protein Science (CIPSM), Butenandtstrasse 5-13, 83177 Munich, Germany
| | - Laura Osorio-Planes
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, 43007 Tarragona, Spain
| | - Phillip L. Geissler
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical Sciences, Physical Biosciences, and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, United States
| | - Michael Groll
- Department of Chemistry, Technical University Munich and Munich Center for Integrated Protein Science (CIPSM), Lichtenbergstr. 4, 85747 Garching/Munich, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilian-University Munich and Munich Center for Integrated Protein Science (CIPSM), Butenandtstrasse 5-13, 83177 Munich, Germany
| | - Johannes Broichhagen
- Department of Chemistry, Ludwig-Maximilian-University Munich and Munich Center for Integrated Protein Science (CIPSM), Butenandtstrasse 5-13, 83177 Munich, Germany
| |
Collapse
|
27
|
Klymko K, Geissler PL, Garrahan JP, Whitelam S. Rare behavior of growth processes via umbrella sampling of trajectories. Phys Rev E 2018; 97:032123. [PMID: 29776178 DOI: 10.1103/physreve.97.032123] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 06/08/2023]
Abstract
We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space, in terms of their typical and atypical trajectories. Thus key features of growth processes can be insensitive to the precise form of the rate constants used to generate them, recalling the insensitivity to microscopic details of certain equilibrium behavior. We obtained these results using a sampling method, inspired by the "s-ensemble" large-deviation formalism, that amounts to umbrella sampling in trajectory space. The method is a simple variant of existing approaches, and applies to ensembles of trajectories controlled by the total number of events. It can be used to determine large-deviation rate functions for trajectory observables in or out of equilibrium.
Collapse
Affiliation(s)
- Katherine Klymko
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | - Juan P Garrahan
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, England, United Kingdom
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| |
Collapse
|
28
|
Schwierz N, Frost CV, Geissler PL, Zacharias M. From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations. J Phys Chem B 2017; 121:671-682. [DOI: 10.1021/acs.jpcb.6b10189] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadine Schwierz
- Department
of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt am Main, Germany
| | - Christina V. Frost
- Physik
Department, Technische Universität München, 85748 Garching, Germany
| | - Phillip L. Geissler
- Chemistry
Department, University of California, Berkeley, California 94720, United States
| | - Martin Zacharias
- Physik
Department, Technische Universität München, 85748 Garching, Germany
| |
Collapse
|
29
|
Ye X, Jones MR, Frechette LB, Chen Q, Powers AS, Ercius P, Dunn G, Rotskoff GM, Nguyen SC, Adiga VP, Zettl A, Rabani E, Geissler PL, Alivisatos AP. Single-particle mapping of nonequilibrium nanocrystal transformations. Science 2016; 354:874-877. [DOI: 10.1126/science.aah4434] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/14/2016] [Indexed: 01/19/2023]
|
30
|
Klymko K, Geissler PL, Whitelam S. Microscopic origin and macroscopic implications of lane formation in mixtures of oppositely driven particles. Phys Rev E 2016; 94:022608. [PMID: 27627361 DOI: 10.1103/physreve.94.022608] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 11/07/2022]
Abstract
Colloidal particles of two types, driven in opposite directions, can segregate into lanes [Vissers et al., Soft Matter 7, 2352 (2011)1744-683X10.1039/c0sm01343a]. This phenomenon can be reproduced by two-dimensional Brownian dynamics simulations of model particles [Dzubiella et al., Phys. Rev. E 65, 021402 (2002)1063-651X10.1103/PhysRevE.65.021402]. Here we use computer simulation to assess the generality of lane formation with respect to variation of particle type and dynamical protocol. We find that laning results from rectification of diffusion on the scale of a particle diameter: oppositely driven particles must, in the time taken to encounter each other in the direction of the drive, diffuse in the perpendicular direction by about one particle diameter. This geometric constraint implies that the diffusion constant of a particle, in the presence of those of the opposite type, grows approximately linearly with the Péclet number, a prediction confirmed by our numerics over a range of model parameters. Such environment-dependent diffusion is statistically similar to an effective interparticle attraction; consistent with this observation, we find that oppositely driven nonattractive colloids display features characteristic of the simplest model system possessing both interparticle attractions and persistent motion, the driven Ising lattice gas [Katz, Leibowitz, and Spohn, J. Stat. Phys. 34, 497 (1984)JSTPBS0022-471510.1007/BF01018556]. These features include long-ranged correlations in the disordered regime, a critical regime characterized by a change in slope of the particle current with the Péclet number, and fluctuations that grow with system size. By analogy, we suggest that lane formation in the driven colloid system is a phase transition in the macroscopic limit, but that macroscopic phase separation would not occur in finite time upon starting from disordered initial conditions.
Collapse
Affiliation(s)
- Katherine Klymko
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| |
Collapse
|
31
|
Abstract
The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. We describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. We show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of the protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon.
Collapse
Affiliation(s)
- Todd R Gingrich
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Chemistry, University of California, Berkeley, CA 94720;
| | - Grant M Rotskoff
- Biophysics Graduate Group, University of California, Berkeley, CA 94720
| | - Gavin E Crooks
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Kavli Energy NanoSciences Institute, Berkeley, CA 94720
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, CA 94720; Biophysics Graduate Group, University of California, Berkeley, CA 94720; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
32
|
Schmid EM, Bakalar MH, Choudhuri K, Weichsel J, Ann H, Geissler PL, Dustin ML, Fletcher DA. Size-dependent protein segregation at membrane interfaces. Nat Phys 2016; 12:704-711. [PMID: 27980602 PMCID: PMC5152624 DOI: 10.1038/nphys3678] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 01/29/2016] [Indexed: 05/21/2023]
Abstract
Membrane interfaces formed at cell-cell junctions are associated with characteristic patterns of membrane protein organization, such as E-cadherin enrichment in epithelial junctional complexes and CD45 exclusion from the signaling foci of immunological synapses. To isolate the role of protein size in these processes, we reconstituted membrane interfaces in vitro using giant unilamellar vesicles decorated with synthetic binding and non-binding proteins. We show that size differences between binding and non-binding proteins can dramatically alter their organization at membrane interfaces in the absence of active contributions from the cytoskeleton, with as little as a ~5 nm increase in non-binding protein size driving its exclusion from the interface. Combining in vitro measurements with Monte Carlo simulations, we find that non-binding protein exclusion is also influenced by lateral crowding, binding protein affinity, and thermally-driven membrane height fluctuations that transiently limit access to the interface. This simple, sensitive, and highly effective means of passively segregating proteins has implications for signaling at cell-cell junctions and protein sorting at intracellular contact points between membrane-bound organelles.
Collapse
Affiliation(s)
- Eva M Schmid
- Department of Bioengineering, University of California, Berkeley, CA
| | - Matthew H Bakalar
- UC Berkeley / UC San Francisco Graduate Group in Bioengineering, Berkeley, CA
| | - Kaushik Choudhuri
- Skirball Institute, New York University School of Medicine, New York, NY
| | - Julian Weichsel
- Department of Chemistry, University of California, Berkeley, CA
| | - HyoungSook Ann
- Department of Bioengineering, University of California, Berkeley, CA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, CA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Michael L Dustin
- Skirball Institute, New York University School of Medicine, New York, NY
- Kennedy Institute, NDORMS, University of Oxford, Oxford, UK
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA
- UC Berkeley / UC San Francisco Graduate Group in Bioengineering, Berkeley, CA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- To whom correspondence should be addressed: Daniel Fletcher ()
| |
Collapse
|
33
|
Abstract
Tubular protrusions are a common feature of living cells, arising from polymerization of stiff protein filaments against a comparably soft membrane. Although this process involves many accessory proteins in cells, in vitro experiments indicate that similar tube-like structures can emerge without them, through spontaneous bundling of filaments mediated by the membrane. Using theory and simulation of physical models, we have elaborated how nonequilibrium fluctuations in growth kinetics and membrane shape can yield such protrusions. Enabled by a new grand canonical Monte Carlo method for membrane simulation, our work reveals a cascade of dynamical transitions from individually polymerizing filaments to highly cooperatively growing bundles as a dynamical bottleneck to tube formation. Filament network organization as well as adhesion points to the membrane, which bias filament bending and constrain membrane height fluctuations, screen the effective attractive interactions between filaments, significantly delaying bundling and tube formation.
Collapse
Affiliation(s)
- Julian Weichsel
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California, United States of America
| |
Collapse
|
34
|
Widmer-Cooper A, Geissler PL. Ligand-Mediated Interactions between Nanoscale Surfaces Depend Sensitively and Nonlinearly on Temperature, Facet Dimensions, and Ligand Coverage. ACS Nano 2016; 10:1877-87. [PMID: 26756464 DOI: 10.1021/acsnano.5b05569] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanoparticles are often covered in ligand monolayers, which can undergo a temperature-dependent order-disorder transition that switches the particle-particle interaction from repulsive to attractive in solution. In this work, we examine how changes in the ligand surface coverage and facet dimensions affect the ordering of ligands, the arrangement of nearby solvent molecules, and the interaction between ligand monolayers on different particles. In particular, we consider the case of strongly bound octadecyl ligands on the (100) facet of CdS in the presence of an explicit n-hexane solvent. Depending on the facet dimensions and surface coverage, we observe three distinct ordered states that differ in how the ligands are packed together, and which affect the thickness of the ligand shell and the structure of the ligand-solvent interface. The temperature dependence of the order-disorder transition also broadens and shifts to lower temperature in a nonlinear manner as the nanoscale is approached from above. We find that ligands on nanoscale facets can behave very similarly to those on macroscopic surfaces in solution, and that some facet dimensions affect the ligand alignment more strongly than others. As the ligands order, the interaction between opposing monolayers becomes attractive, even well below full surface coverage. The strength of attraction per unit surface area is strongly affected by ligand coverage, but only weakly by facet width. Conversely, we find that bringing two monolayers together just above the order-disorder transition temperature can induce ordering and attraction.
Collapse
Affiliation(s)
- Asaph Widmer-Cooper
- School of Chemistry, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Phillip L Geissler
- Department of Chemistry, University of California Berkeley , Berkeley, California 94720, United States
| |
Collapse
|
35
|
Abstract
Demixing can occur in systems of two or more particle species that experience different driving forces, e.g., mixtures of self-propelled active particles or of oppositely charged colloids subject to an electric field. Here we show with macroscopic experiments and computer simulations that the forces underlying such non-equilibrium segregation can be used to control the self-assembly of particles that lack attractive interactions. We demonstrate that, depending on the direction, amplitude and frequency of a periodic external force acting on one particle species, the structures formed by a second, undriven species can range from compact clusters to elongated, string-like patterns.
Collapse
Affiliation(s)
- Michael Grünwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| | | | | | | |
Collapse
|
36
|
Schwierz N, Frost CV, Geissler PL, Zacharias M. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc 2016; 138:527-39. [PMID: 26694883 DOI: 10.1021/jacs.5b08717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.
Collapse
Affiliation(s)
- Nadine Schwierz
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Christina V Frost
- Physik Department, Technische Universität München , 85748 Garching, Germany
| | - Phillip L Geissler
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Martin Zacharias
- Physik Department, Technische Universität München , 85748 Garching, Germany
| |
Collapse
|
37
|
Abstract
Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective on Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this "noise guidance" synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.
Collapse
Affiliation(s)
- Todd R Gingrich
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
38
|
Noriega R, Finley DT, Haberstroh J, Geissler PL, Francis MB, Ginsberg NS. Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity. J Phys Chem B 2015; 119:6963-73. [PMID: 26035585 DOI: 10.1021/acs.jpcb.5b03784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.
Collapse
Affiliation(s)
| | | | | | | | | | - Naomi S Ginsberg
- ∇Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
| |
Collapse
|
39
|
Abstract
Folded protein structures are both stable and dynamic. Historically, our clearest window into these structures came from X-ray crystallography, which generally provided a static image of each protein's singular "folded state", highlighting its stability. Deviations away from that crystallographic structure were difficult to quantify, and as a result, their potential functional consequences were often neglected. However, several dynamical and statistical studies now highlight the structural variability that is present within the protein's folded state. Here we review mounting evidence of the importance of these structural rearrangements; both experiment and computation indicate that folded proteins undergo substantial fluctuations that can greatly influence their function. Crucially, recent studies have shown that structural elements of proteins, especially their side-chain degrees of freedom, fluctuate in ways that generate significant conformational heterogeneity. The entropy associated with these motions contributes to the folded structure's thermodynamic stability. In addition, since these fluctuations can shift in response to perturbations such as ligand binding, they may play an important role in the protein's capacity to respond to environmental cues. In one compelling example, the entropy associated with side-chain fluctuations contributes significantly to regulating the binding of calmodulin to a set of peptide ligands. The neglect of fluctuations within proteins' native states was often justified by the dense packing within folded proteins, which has inspired comparisons with crystalline solids. Many liquids, however, can achieve similarly dense packing yet fluidity is maintained through correlated molecular motions. Indeed, the studies we discuss favor comparison of folded proteins not with solids but instead with dense liquids, where the internal side chain fluidity is facilitated by collective motions that are correlated over long distances. These correlated rearrangements can enable allosteric communication between different parts of a protein, through subtle and varied channels. Such long-range correlations appear to be an innate feature of proteins in general, manifest even in molecules lacking known allosteric regulators and arising robustly from the physical nature of their internal environment. Given their ubiquity, it is only to be expected that, over time, nature has refined some subset of these correlated motions and put them to use. Native state fluctuations increasingly appear to be vital for proteins' natural functions. Understanding the diversity, origin, and range of these rearrangements may provide novel routes for rationally manipulating biomolecular activity.
Collapse
Affiliation(s)
- Kateri H. DuBay
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Gregory R. Bowman
- Department
of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Phillip L. Geissler
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
40
|
Abstract
Many forms of cell motility rely on Brownian ratchet mechanisms that involve multiple stochastic processes. We present a computational and theoretical study of the nonequilibrium statistical dynamics of such a many-body ratchet, in the specific form of a growing polymer gel that pushes a diffusing obstacle. We find that oft-neglected correlations among constituent filaments impact steady-state kinetics and significantly deplete the gel's density within molecular distances of its leading edge. These behaviors are captured quantitatively by a self-consistent theory for extreme fluctuations in filaments' spatial distribution.
Collapse
Affiliation(s)
- Evan Hohlfeld
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | |
Collapse
|
41
|
Gingrich TR, Vaikuntanathan S, Geissler PL. Heterogeneity-induced large deviations in activity and (in some cases) entropy production. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 90:042123. [PMID: 25375454 DOI: 10.1103/physreve.90.042123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 06/04/2023]
Abstract
We solve a simple model that supports a dynamic phase transition and show conditions for the existence of the transition. Using methods of large deviation theory we analytically compute the probability distribution for activity and entropy production rates of the trajectories on a large ring with a single heterogeneous link. The corresponding joint rate function demonstrates two dynamical phases--one localized and the other delocalized, but the marginal rate functions do not always exhibit the underlying transition. Symmetries in dynamic order parameters influence the observation of a transition, such that distributions for certain dynamic order parameters need not reveal an underlying dynamical bistability. Solution of our model system furthermore yields the form of the effective Markov transition matrices that generate dynamics in which the two dynamical phases are at coexistence. We discuss the implications of the transition for the response of bacterial cells to antibiotic treatment, arguing that even simple models of a cell cycle lacking an explicit bistability in configuration space will exhibit a bistability of dynamical phases.
Collapse
Affiliation(s)
- Todd R Gingrich
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
42
|
Onoa B, Schneider AR, Brooks MD, Grob P, Nogales E, Geissler PL, Niyogi KK, Bustamante C. Atomic force microscopy of photosystem II and its unit cell clustering quantitatively delineate the mesoscale variability in Arabidopsis thylakoids. PLoS One 2014; 9:e101470. [PMID: 25007326 PMCID: PMC4090009 DOI: 10.1371/journal.pone.0101470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/06/2014] [Indexed: 11/25/2022] Open
Abstract
Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arrays according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets.
Collapse
Affiliation(s)
- Bibiana Onoa
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Anna R. Schneider
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
| | - Matthew D. Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Patricia Grob
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Eva Nogales
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Phillip L. Geissler
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Carlos Bustamante
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Department of Physics, University of California, Berkeley, California, United States of America
- Kavli Energy NanoSciences Institute at the University of California, Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
43
|
Grünwald M, Geissler PL. Patterns without patches: hierarchical self-assembly of complex structures from simple building blocks. ACS Nano 2014; 8:5891-7. [PMID: 24816138 PMCID: PMC4071109 DOI: 10.1021/nn500978p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/12/2014] [Indexed: 05/26/2023]
Abstract
Nanoparticles with "sticky patches" have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they could form. Using computer simulations, we show that structures of the same genre can be obtained from a solution of simple isotropic spheres, with control only over their sizes and a small number of binding affinities. In a first step, finite clusters of well-defined structure and composition emerge from natural dynamics with high yield. In effect a kind of patchy particle, these clusters can further assemble into a variety of complex superstructures, including filamentous networks, ordered sheets, and highly porous crystals.
Collapse
Affiliation(s)
- Michael Grünwald
- Computational Physics, University of Vienna, Sensengasse 8, 1090 Vienna, Austria
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
44
|
Vaikuntanathan S, Gingrich TR, Geissler PL. Dynamic phase transitions in simple driven kinetic networks. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:062108. [PMID: 25019726 DOI: 10.1103/physreve.89.062108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 06/03/2023]
Abstract
We analyze the probability distribution for entropy production rates of trajectories evolving on a class of out-of-equilibrium kinetic networks. These networks can serve as simple models for driven dynamical systems, where energy fluxes typically result in nonequilibrium dynamics. By analyzing the fluctuations in the entropy production, we demonstrate the emergence, in a large system size limit, of a dynamic phase transition between two distinct dynamical regimes.
Collapse
Affiliation(s)
| | - Todd R Gingrich
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
45
|
Abstract
![]()
Basic
principles of statistical mechanics require that proteins
sample an ensemble of conformations at any nonzero temperature. However,
it is still common to treat the crystallographic structure of a protein
as the structure of its native state, largely because
high-resolution structural characterization of protein flexibility
remains a profound challenge. To assess the typical degree of conformational
heterogeneity within folded proteins, we construct Markov state models
describing the thermodynamics and kinetics of proteins ranging from
72 to 263 residues in length. Each of these models is built from hundreds
of microseconds of atomically detailed molecular dynamics simulations.
Examination of the side-chain degrees of freedom reveals that almost
every residue visits at least two rotameric states over this time
frame, with rotamer transition rates spanning a wide range of time
scales (from nanoseconds to tens of microseconds). We also report
substantial backbone dynamics on time scales longer than are typically
addressed by experimental measures of protein flexibility, such as
NMR order parameters. Finally, we demonstrate that these extensive
rearrangements are consistent with NMR and crystallographic data,
which supports the validity of our models. Altogether, these results
depict the interior of proteins not as well-ordered solids, as is
often imagined, but instead as dense fluids, which undergo substantial
structural fluctuations despite their high packing fraction.
Collapse
Affiliation(s)
- Gregory R Bowman
- Departments of Molecular & Cell Biology and ‡Chemistry, University of California , Berkeley, California 94720, United States
| | | |
Collapse
|
46
|
Mey ASJS, Geissler PL, Garrahan JP. Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:032109. [PMID: 24730792 DOI: 10.1103/physreve.89.032109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Indexed: 06/03/2023]
Abstract
We explore the dynamical large deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of nonequilibrium dynamical phase transitions in ensembles of trajectories between active and inactive dynamical phases, whose nature depends on the properties of the interaction potential. We consider three potentials: two heterogeneous interaction potentials and a homogeneous Gō potential. When preserving the full heterogeneity of interactions due to a given amino acid sequence, either in a fully interacting model or in a native contacts interacting model (heterogeneous Gō model), the observed dynamic transitions occur between equilibrium highly native states and highly native but kinetically trapped states. A native activity is defined that allows us to distinguish these dynamic phases. In contrast, for the homogeneous Gō model, where all native interaction energies are uniform and the amino acid sequence plays no role, the dynamical transition is a direct consequence of the static bistability between the unfolded and the native state. In the two heterogeneous interaction models the native-active and native-inactive states, despite their thermodynamic similarity, have widely varying dynamical properties, and the transition between them occurs even in lattice proteins whose sequences are designed to make them optimal folders.
Collapse
Affiliation(s)
- Antonia S J S Mey
- School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Phillip L Geissler
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA and Chemical Sciences and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Juan P Garrahan
- School of Physics & Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| |
Collapse
|
47
|
Schneider AR, Geissler PL. Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities. Front Plant Sci 2014; 4:555. [PMID: 24478781 PMCID: PMC3896813 DOI: 10.3389/fpls.2013.00555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/30/2013] [Indexed: 06/03/2023]
Abstract
Coarse-grained simulation is a powerful and well-established suite of computational methods for studying structure and dynamics in nanoscale biophysical systems. As our understanding of the plant photosynthetic apparatus has become increasingly nuanced, opportunities have arisen for coarse-grained simulation to complement experiment by testing hypotheses and making predictions. Here, we give an overview of best practices in coarse-grained simulation, with a focus on techniques and results that are applicable to the plant thylakoid membrane-protein system. We also discuss current research topics for which coarse-grained simulation has the potential to play a key role in advancing the field.
Collapse
Affiliation(s)
- Anna R. Schneider
- Biophysics Graduate Group, University of CaliforniaBerkeley, CA, USA
- Department of Chemistry, University of CaliforniaBerkeley, CA, USA
| | - Phillip L. Geissler
- Department of Chemistry, University of CaliforniaBerkeley, CA, USA
- Chemical Sciences and Physical Biosciences Divisions, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| |
Collapse
|
48
|
Vaikuntanathan S, Geissler PL. Putting water on a lattice: the importance of long wavelength density fluctuations in theories of hydrophobic and interfacial phenomena. Phys Rev Lett 2014; 112:020603. [PMID: 24483999 DOI: 10.1103/physrevlett.112.020603] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Indexed: 06/03/2023]
Abstract
The physics of air-water interfaces plays a central role in modern theories of the hydrophobic effect. Implementing these theories, however, has been hampered by the difficulty of addressing fluctuations in the shape of such soft interfaces. We show that this challenge is a fundamental consequence of mapping long wavelength density variations onto discrete degrees of freedom. Drawing from studies of surface roughness in lattice models, we account for the resulting nonlinearities simply but accurately. Simulations show that this approach captures complex solvation behaviors quantitatively.
Collapse
Affiliation(s)
| | - Phillip L Geissler
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
49
|
Vaikuntanathan S, Shaffer PR, Geissler PL. Adsorption of solutes at liquid-vapor interfaces: insights from lattice gas models. Faraday Discuss 2013; 160:63-74; discussion 103-20. [PMID: 23795493 DOI: 10.1039/c2fd20106b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption behavior of ions at liquid-vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of polar solvents, contrary to predictions of classical theories. Motivated by this generality, and by the simple physical ingredients implicated by computational studies, we have examined interfacial solvation in highly schematic models, which resolve only coarse fluctuations in solvent density and cohesive energy. Here we show that even such lattice gas models recapitulate surprising thermodynamic trends observed in detailed simulations and experiments. Attention is focused on the case of two dimensions, for which approximate energy and entropy profiles can be calculated analytically. Simulations and theoretical analysis of the lattice gas highlight the role of capillary wave-like fluctuations in mediating adsorption. They further point to ranges of temperature and solute-solvent interaction strength where surface propensity is expected to be strongest.
Collapse
|
50
|
Grünwald M, Lutker K, Alivisatos AP, Rabani E, Geissler PL. Metastability in pressure-induced structural transformations of CdSe/ZnS core/shell nanocrystals. Nano Lett 2013; 13:1367-1372. [PMID: 22800435 DOI: 10.1021/nl3007165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The kinetics and thermodynamics of structural transformations under pressure depend strongly on particle size due to the influence of surface free energy. By suitable design of surface structure, composition, and passivation it is possible, in principle, to prepare nanocrystals in structures inaccessible to bulk materials. However, few realizations of such extreme size-dependent behavior exist. Here, we show with molecular dynamics computer simulation that in a model of CdSe/ZnS core/shell nanocrystals the core high-pressure structure can be made metastable under ambient conditions by tuning the thickness of the shell. In nanocrystals with thick shells, we furthermore observe a wurtzite to NiAs transformation, which does not occur in the pure bulk materials. These phenomena are linked to a fundamental change in the atomistic transformation mechanism from heterogeneous nucleation at the surface to homogeneous nucleation in the crystal core.
Collapse
Affiliation(s)
- Michael Grünwald
- Department of Chemistry, University of California, Berkeley, California 94720, United States.
| | | | | | | | | |
Collapse
|