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A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational…
Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing…
Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and…
Molecule- and solid-state gears build the elementary constituents of nanoscale mechanical machineries. Recent experimental advances in fabrication technologies in the field have strongly contributed to better delineate the roadmap towards…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We study a Markov random process describing a muscle molecular motor behavior. Every motor is either bound up with a thin filament or unbound. In the bound state the motor creates a force proportional to its displacement from the neutral…
Molecular motors work collectively to transport cargo within cells, with anywhere from one to several hundred motors towing a single cargo. For a broad class of collective-transport systems, we use tools from stochastic thermodynamics to…
An inchworm processive mechanism is proposed to explain the motion of dimeric molecular motors such as kinesin. We present here preliminary results for this mechanism focusing on observables like mean velocity, coupling ratio and efficiency…
Manipulating and coupling molecule gears is the first step towards realizing molecular-scale mechanical machines. Here, we theoretically investigate the behavior of such gears using molecular dynamics simulations. Within a nearly rigid-body…
Kinetics of model catalytic processes proceeding on inhomogeneous surfaces is studied. We employ an extended mean-field model that takes into account surface inhomogeneities. The influence of surface diffusion of adsorbent on the kinetics…
Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Motivated by the numerous healthcare applications of molecular communication (MC) inside blood vessels, this work considers relay/cooperative nanomachine (CN)-assisted mobile MC between a source nanomachine (SN) and a destination…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
Lubricants are widely used in macroscopic mechanical systems to reduce friction and wear. However, on the microscopic scale, it is not clear to what extent lubricants are beneficial. Therefore, in this study, we consider two diamond…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in…
Synthetic active colloidal systems are being studied extensively because of the diverse and often unusual phenomena these nonequilibrium systems manifest, and their potential applications in fields ranging from biology to material science.…