arXiv subjects

Somajit Dey

Publications and source records attributed to Somajit Dey.

7 recordsLinked to original sources

arXiv2021

SiMPLISTIC: A Novel Pairwise Potential for Implicit Solvent Lipid Simulations with Single-site Models

Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller number of interaction sites in the model molecules, and the lack of fast sub-molecular degrees of freedom. In this paper, we describe a maximally coarse-grained model for lipids in implicit water. The model is called SiMPLISTIC, which abbreviates for Single-site Model with Pairwise interaction for Lipids in Implicit Solvent with Tuneable Intrinsic Curvature. SiMPLISTIC lipids rapidly self-assemble into realistic non-lamellar and lamellar phases such as inverted micelles and bilayers, the spontaneous curvature of the phase being determined by a single free parameter of the model. Model membrane simulations with the lamellar lipids show satisfactory fluid and gel phases with no interdigitation or tilt. The model lipids follow rigid body dynamics suggested by empirical studies, and generate bilayer elastic properties consistent with experiments and other simulations. SiMPLISTIC can also simulate mixtures of lipids that differ in their packing parameter or length, the latter leading to the phenomenon of hydrophobic mismatch driven domain formation. The model has a large scope due to its speed, conceptual and computational simplicity, and versatility. Applications may range from large-scale simulations for academic and industrial research on various lipid-based systems, such as lyotropic liquid crystals, biological and biomimetic membranes, vectors for drug and gene delivery, to fast, lightweight, interactive simulations for gaining insights into self-assembly, lipid polymorphism, biomembrane organization etc.

cond-mat.soft↗

arXiv2020

Minimal Modification to Nosé-Hoover Barostat Enables Correct NPT Sampling

The Nosé-Hoover dynamics for isothermal-isobaric (NPT) computer simulations do not generate the appropriate partition function for ergodic systems. The present paper points out that this can be corrected with a simple addition of a constant term to only one of the equations of motion. The solution proposed is much simpler than previous modifications done towards the same goal. The present modification is motivated by the work virial theorem, which has been derived for the special case of an infinitely periodic system in the first part of this paper.

physics.comp-ph↗

arXiv2019

Minimal Coarse-Grained Modelling Towards Implicit-Solvent Simulation of Generic Bolaamphiphiles

A simple, dual-site model of bolaamphiphiles (bolaforms or bipolar amphiphiles) is developed based on an earlier single-site model of (monopolar) amphiphiles [S. Dey, J. Saha, Phys. Rev. E 95, 023315 (2017)]. The model incorporates aqueous environment (both hydrophobic effect and hydration force) in its anisotropic site-site interactions, thus obviating the need to simulate solvent particles explicitly. This economy of sites and the absence of explicit solvent particles enable molecular dynamics simulations of bolaamphiphiles to achieve mesoscopic length and time-scales unattainable by any bead-spring model or explicit solvent computations. The model applies to generic bolas only, since the gain in scale can only be obtained by sacrificing the resolution of detailed molecular structure. Thanks to dual-sites, however, (as opposed to a single-site model) our model can incorporate the essential flexibility of bolas that leads to their U-conformers. The model bolas show successful self-assembly into experimentally observed nano-structures like micelles, rods, lamellae etc. and retain fluidity in very stable monolayers. Presence of membrane-spanning model bolas in bilayers of model monopolar amphiphiles increases the stability and impermeability of the lamellar phase. Model bolas are also seen to be less diffusive and to produce thicker layers compared to their monopolar counterparts. Rigid model bolas, though achiral themselves, show self-assembly into helical rods. As all these observations agree with the well-known key characteristics of archaeal lipids and synthetic bolaamphiphiles, our model promises to be effective for studies of bolas in context of biomimetics, drug-delivery and low molecular weight hydrogelators. To the best of our knowledge, no other single or dual-site, solvent-free model for bolas has been reported thus far.

cond-mat.soft↗

arXiv2018

Time-Reversible, Symplectic, Angular Velocity Based Integrator for Rigid Linear Molecules

A very simple explicit integrator for the rotational motion of rigid linear molecules is presented which can preserve the rigidity of the molecules without requiring any constraint force. The integrator is time-reversible and symplectic, thus preserving volume in phase space. It also conserves angular momentum. As expected, having all these virtues, it remains stable for large time-steps. Both the leap-frog and velocity-Verlet versions of the integrator are described. Since it features angular velocities explicitly, the integrator can be conveniently coupled to different thermostats. As a specific example, the Nose-Hoover thermostatting is discussed in detail to aid ready implementation. A simpler and faster adaptation of the main integrator, appropriate for double precision computing, is also offered.

physics.comp-ph↗

arXiv2017

Time Isotropy, Lorentz Transformation and Inertial Frames

Homogeneity of space and time, spatial isotropy, principle of relativity and the existence of a finite speed limit (or its variants) are commonly believed to be the only axioms required for developing the special theory of relativity (Lorentz transformations). In this paper it is shown, however, that Lorentz transformation cannot actually be derived without the explicit assumption of time isotropy (time-reversal symmetry) which is logically independent of the other postulates of relativity. Postulating time isotropy also restores the symmetry between space and time in the postulates of relativity. Inertial frames are defined in influential texts as frames having space-time homogeneity and spatial isotropy only. Inclusion of time isotropy in that definition is also suggested.

physics.class-ph↗

arXiv2017

Special Relativity (Lorentz Transformation) Follows from the Definition of Inertial Frames

Besides the defining space-time symmetries (homogeneity and isotropy) of inertial frames, the derivation of Lorentz transformation requires postulating the principle of relativity and the existence of a finite speed limit. In this article, we point out that the existence of a finite speed limit can be readily inferred from the nature of allowed inertial frames. We also show that the principle of relativity can be obtained from the defining space-time symmetries of every inertial frame. Therefore, if the conventional definition of inertial frames is augmented properly, the special theory of relativity (Lorentz transformation) would follow from the definition of inertial frames.

physics.class-ph↗

arXiv2016

Simple, self-assembling, single-site model amphiphile for water-free simulation of lyotropic phases

Computationally, low-resolution coarse-grained models provide the most viable means for simulating the large length and time scales associated with mesoscopic phenomena. Moreover, since lyotropic phases in solution may contain high solvent to amphiphile ratio, implicit solvent models are appropriate for many purposes. By modifying the well-known Gay-Berne potential with an imposed uni-directionality and a longer range, we have come to a simple single-site model amphiphile that can rapidly self-assemble to give diverse lyotropic phases without the explicit incorporation of solvent particles. The model represents a tuneable packing parameter that manifests in the spontaneous curvature of amphiphile aggregates. Apart from large scale simulations (e.g. the study of self-assembly, amphiphile mixing, domain formation etc.) this novel, non-specific model may be useful for suggestive pilot projects with modest computational resources. No such self-assembling, single-site amphiphile model has been reported previously in the literature to the best of our knowledge.

cond-mat.soft↗