Related papers: Lipid thermodynamics : melting is molecular
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereo-isomers, even at very low temperatures. In this paper we discuss the different approaches for the manipulation of the motion of…
We present a quantum mechanical / molecular mechanics (QM/MM) to tackle chemical reactions with substantial molecular reorganization. For this, molecular dynamics simulations with smoothly switched interaction models are used to suggest…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
Thermodynamics could be seen as an expression of physics at a high epistemic level. As such, its potential as an inductive bias to help machine learning procedures attain accurate and credible predictions has been recently realized in many…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
Proteinoids -- thermal proteins -- are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Years ago Edwards proposed a thermodynamic description of dense granular matter, in which the grains (the `atoms' of the system) interact with inelastic forces. The approach is intriguing but is not justified from first principles, and…
We investigate the slow dynamics in gelling systems by means of MonteCarlo simulations on the cubic lattice of a minimal statistical mechanics model. By opportunely varying some model parameter we are able to describe a crossover from the…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
We construct a thermodynamic model for theoretical calculation of the boiling process of multicomponent mixtures of hydrocarbons (e.g., crude oil). The model governs kinetics of the mixture composition in the course of the distillation…
Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…
The morphometric approach is a powerful ansatz for decomposing the chemical potential for a complex solute into purely geometrical terms. This method has proven accuracy in hard spheres, presenting an alternative to comparatively expensive…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…