Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics, and their biological function. Currently, it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome "collective variable" enhanced sampling protocols. Here, we describe a framework that combines ensemble MD simulations and virtual reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables a priori. We further show that eMD-VR generated pathways can be combined with Markov state models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts.

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures "on the fly" and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human–computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3–4 orders of magnitude.

Effect of esthetic illusions on rhinoplasty assessment

OBJECTIVE

Esthetic assessment in rhinoplasty represents a balance between art and science. The result of surgical maneuvres in creating esthetic illusions has been alluded to, but has never been scientifically reported. This project analyzed the effect of optical illusions in esthetic assessment.

METHOD

Eight rhinoplasty case studies were designed using computer imaging. Two hundred and ten judges analyzed the apparent differences in one parameter, such as tip projection, tip rotation, dorsal hump, and nasal size, when a different parameter was altered.

RESULTS

This study confirms the validity of nasal esthetic illusions. These results indicate how surgical maneuvres that vary one parameter can create the illusion of a variation in tip projection or tip rotation.

CONCLUSIONS

The surgeon can exploit esthetic illusions to provide greater control over rhinoplasty dynamics.

Adjuvant radiotherapy following neck dissection and parotidectomy for metastatic malignant melanoma

BACKGROUND

Regional recurrence remains a problem in the management of patients with metastatic malignant melanoma in the cervical lymph nodes and parotid. In this study, the influence of the number of positive nodes, extracapsular spread, and the use of adjuvant radiotherapy on regional control and survival were analyzed.

METHODS

A non-randomized, prospectively documented series of 143 patients with histologically positive nodes in the neck or parotid was analyzed. There were 152 dissected necks or parotids: 45 of these received postoperative radiotherapy, 6 x 5.5 Gy fractions over 3 weeks; 107 were not irradiated.

RESULTS

The regional recurrence rate was 6.5% in the irradiated group, compared with 18.7% in the non-irradiated group (p = .055). The irradiated group, however, had more extensive nodal involvement than the non-irradiated group: 65% had two or more positive nodes, and 48% had extracapsular spread, compared with 40% and 19%, respectively, in the non-irradiated group. Survival was significantly worse when there was extracapsular spread (p < .05) or multiple node involvement (p < .01). By multivariate analysis, the use of adjuvant radiotherapy was associated with a trend toward improved regional control (p = .065), but survival was not improved.

CONCLUSIONS

Adjuvant radiotherapy was associated with improved control of metastatic malignant melanoma in the neck and parotid; however, statistical significance was not reached. A prospective trial should be supported to clarify this question.

A prospective study of the effect of fundoplication on primary and secondary peristalsis in the esophagus

We studied 13 patients before and after Nissen fundoplication and compared them with 11 healthy volunteers and 12 other patients with dysphagia after fundoplication. Esophageal manometry was performed to assess primary and secondary peristalsis induced by esophageal distention with air and water boluses. In patients with reflux disease, secondary peristalsis was initiated at a median rate of 60% of distending episodes, propagation of the secondary peristaltic wave occurred in 40% and lower oesophageal sphincter relaxation occurred with 70% of secondary peristaltic waves. Fundoplication did not alter the initiation or propagation rate of secondary peristalsis but it decreased the median lower esophageal sphincter relaxation rate to 45% (P < 0.03). Fundoplication was not associated with a change in the amplitude of primary peristaltic waves even in patients complaining of dysphagia. In post-fundoplication patients, successful secondary peristaltic waves had significantly lower (P < 0.005) proximal and distal amplitude than primary peristaltic waves. We conclude that there is no improvement in primary or secondary peristalsis after fundoplication and dysphagia after fundoplication is not due to altered peristalsis.

Left ventricular false aneurysm after previous repair of acquired ventricular septal defect

We report a novel case of a 69-year-old woman who was treated surgically for a postinfarction inferior ventricular septal defect and presented 3 years postoperatively with a large left ventricular false aneurysm. This was successfully repaired.