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Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The exact formulation of the path integral centroid dynamics is extended to include composites of the position and momentum operators. We present the generalized centroid dynamics (GCD), which provides a basis to calculate Kubo-transformed…
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
Robotics is shifting from rigid, articulated systems to more sophisticated and heterogeneous mechanical structures. Soft robots, for example, have continuously deformable elements capable of large deformations. The flourishing of control…
In this paper, we study modulation instabilities (MI) in a one-dimensional chain configuration of a flexible mechanical metamaterial (flexMM). Using the lumped element approach, flexMMs can be modeled by a coupled system of discrete…
The finite-frequency transport properties of a large-spin molecule attached to ferromagnetic contacts are studied theoretically in the Kondo regime. The focus is on the behavior of the dynamical conductance in the linear response regime,…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Structure and reaction studies with a method of antisymmetrized molecular dynamics (AMD) were reviewed. Applications of time-independent and time-dependent versions of the AMD were described. In applications of time-independent AMD to…
We present a novel efficient implementation of the flexible boundary condition (FBC) method, initially proposed by Sinclair et al., for large single-periodic problems. Efficiency is primarily achieved by constructing a hierarchical matrix…
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the…
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on…
Numerical solutions of the incompressible magnetohydrodynamic (MHD) equations are reported for the interior of a rotating, perfectly-conducting, rigid spherical shell that is insulator-coated on the inside. A previously-reported spectral…
The theoretical justification of the Hybrid Monte Carlo algorithm depends upon the molecular dynamics trajectories within it being exactly reversible. If computations were carried out with exact arithmetic then it would be easy to ensure…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…