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We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
We consider integrated circuits with semiconductors modeled by modified nodal analysis and drift-diffusion equations. The drift-diffusion equations are discretized in space using mixed finite element method. This discretization yields a…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
An elastic spring network is an example of evolvable matter. It can be pruned to couple separated pairs of nodes so that when a strain is applied to one of them, the other responds either in-phase or out-of-phase. This produces two pruned…
Liquid-crystal networks consist of weakly crosslinked polymers that are coupled to liquid-crystal molecules. The resultant hybrid system has rich elastic properties. We develop a phase field model to describe mechanical properties of a…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
We employ a matrix-based solver for the linear rheology of fluid-immersed disordered spring networks to reveal four distinct dynamic response regimes. One regime - completely absent in the known vacuum response - exhibits coupled fluid flow…
We explore the range over which the elasticity of disordered spring networks can be manipulated by the removal of selected bonds. By taking into account the local response of a bond, we demonstrate that the effectiveness of pruning can be…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
At mesoscopic scales electrolyte solutions are modeled by the fluctuating generalized Poisson-Nernst-Planck (PNP) equations [J.-P. P\'eraud et al., Phys. Rev. F, 1(7):074103, 2016]. However, at length and time scales larger than the Debye…
In this paper, a micro-mechanical model is introduce to characterize the stress softening phenomenon in double network hydrogels. Damage in polymer matrices under deformation, which appears as the rupture of cross-linking, is assumed to…
We use the normal mode formalism to study the shear rheology of the vertex model for epithelial tissue mechanics in the overdamped linear response regime. We consider systems with external (e.g., cell-substrate) and internal (e.g.,…
The inter-connection between the elasticity of a dielectric film and the wetting of a sessile drop on the same, under an applied electrical voltage, remains unaddressed. Here, we report the electrowetting-on-dielectric (EWOD) behaviour of…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…
Based on a Hamiltonian that incorporates the elastic coupling between a tracer and active particles, we derive a generalized Langevin model for the non-equilibrium mechanical response of active viscoelastic biomatter. Our model accounts for…
Elastic wave speeds are fundamental in geomechanics and have historically been described by an analytic formula that assumes linearly elastic solid medium. Empirical relations stemming from this assumption were used to determine nonlinearly…
Discrete-state stochastic models are a popular approach to describe the inherent stochasticity of gene expression in single cells. The analysis of such models is hindered by the fact that the underlying discrete state space is extremely…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…