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Contradictory experimental reports on the relationship between efficiency and stimulation frequency have hindered mechanistic understanding in converting neural activity into mechanical work during muscle contraction. To resolve this issue,…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…
The cooperative action of many molecular motors is essential for dynamic processes such as cell motility and mitosis. This action can be studied by using motility assays in which the motion of cytoskeletal filaments over a surface coated…
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales and microscopic details of signal transmission in proteins are…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel…
Flapping wing flight is a challenging dynamical problem and is also a very fascinating subject to study in the field of biomimetic robotics. A Bat, in particular, has a very articulated armwing mechanism with high degrees-of-freedom and…
The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and…
Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
The distribution of galaxies, halo abundance, and peculiar velocities are influenced by non-linear gravitational interactions, making the study of non-linear evolution crucial for accurate cosmological predictions. We explore these aspects…
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more…
Human joint dynamic stiffness plays an important role in the stability of performance augmentation exoskeletons. In this paper, we consider a new frequency domain model of the human joint dynamics which features a complex value stiffness.…
Unfolding is an important procedure in particle physics experiments which corrects for detector effects and provides differential cross section measurements that can be used for a number of downstream tasks, such as extracting fundamental…
The energy level spacing distribution of a tight-binding hamiltonian is monitored across the mobility edge for a fixed disorder strength. Any mixing of extended and localized levels is avoided in the configurational averages, thus…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
In small cell networks, high mobility of users results in frequent handoff and thus severely restricts the data rate for mobile users. To alleviate this problem, we propose to use heterogeneous, two-tier network structure where static users…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…