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Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
The presence of multiple stable states and associated nonlinear phenomena, such as hysteresis, in multistable mechanical metamaterials enables frequency-independent energy harvesting and shock absorption. This study focuses on shock…
We have designed a new method to fit the energy and atomic forces using a single artificial neural network (SANN) for any number of chemical species present in a molecular system. The traditional approach for fitting the potential energy…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Here we propose an NPT metadynamics simulation scheme for pressure-induced structural phase transitions, using coordination number and volume as collective variables, and apply it to the reconstructive structural transformation $B1$-$B2$ in…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
This work describes through semiclassical Boltzmann transport theory and simulation a novel nanostructured material design that can lead to unprecedentedly high thermoelectric power factors, with improvements of more than an order of…
Local drug delivery has received much recognition in recent years, yet it is still unpredictable how drug efficacy depends on physicochemical properties and delivery kinetics. The purpose of the current study is to provide a useful…
We design and analyse an energy stable, structure preserving, well-balanced and asymptotic preserving (AP) scheme for the barotropic Euler system with gravity in the anelastic limit. The key to energy stability is the introduction of…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of…
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a…
We review recent advances in the design, synthesis, and modeling of active fluids. Active fluids have been at the center of many technological innovations and theoretical advances over the past two decades. Research on this new class of…
Active constituents burn fuel to sustain individual motion, giving rise to collective effects that are not seen in systems at thermal equilibrium, such as phase separation with purely repulsive interactions. There is a great potential in…
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Hybrid nanocomposites can offer a wide range of opportunities to control the light-matter interac- tion and electromagnetic energy flow at the nanoscale, leading to exotic optoelectronic devices. We study theoretically the dipole-dipole…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
One of the promising frontiers of bioengineering is the controlled release of a therapeuticdrug from a vehicle across the skin (transdermal drug delivery). In order to study the complete process, a two-phase mathematical model describing…