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We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
In energy intensive industrial systems, an evaporative cooling process may introduce operational flexibility. Such flexibility refers to a systems ability to deviate from its scheduled energy consumption. Identifying the flexibility, and…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
We report detailed theoretical investigations of the micro-mechanics and bulk elastic properties of composites consisting of randomly distributed stiff fibers embedded in an elastic matrix in two and three dimensions. Recent experiments…
The nanomechanical response of a folded single protein, the natural nanomachine responsible for myriad biological processes, provides insight into its function. The conformational flexibility of a folded state, characterized by its…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
Predicting the adsorption affinity of a small molecule to a target surface is of importance to a range of fields, from catalysis to drug delivery and human safety, but a complex task to perform computationally when taking into account the…
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the…
We introduce a tempering approach with stochastic density functional theory (sDFT), labeled t-sDFT, which reduces the statistical errors in the estimates of observable expectation values. This is achieved by rewriting the electronic density…
The ability to accurately model interatomic interactions in large-scale systems is fundamental to understanding a wide range of physical and chemical phenomena, from drug-protein binding to the behavior of next-generation materials. While…
Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability…
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
We study the dynamics of a mean-field Ising model whose coupling depends on the magnetization via a linear feedback function. A key feature of this linear feedback Ising model (FIM) is the possibility of temperature-induced bistability,…
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…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…