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In recent years molecular elasticity has emerged as an active area of research: there are experiments that probe mechanical properties of single biomolecules such as DNA and Actin, with a view to understanding the role of elasticity of…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Biomolecules exhibit dynamic conformations critical to their functions, yet observing these processes at the single-molecule level under native conditions remains a formidable challenge. While surface immobilization has been widely used to…
Biomembranes consisting of two opposing phospholipid monolayers, which comprise the so-called lipid bilayer, are largely responsible for the dual solid-fluid behavior of individual cells and viruses. Quantifying the mechanical…
Molecular-scale interactions between solvated macromolecules and solid surfaces govern a large number of processes, from biology to engineering. Yet, despite extensive characterization at the macroscopic level, our molecular understanding…
The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show…
Microscopic formula to describe the entropy of biomolecular solutions are derived based on the Gibbs formula of entropy, and the generalized Langevin theory combined with the RISM/3D-RISM theory. Two formula are derived: one is concerned…
Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity---hysteresivity normalized to the extremes of an elastic solid or a viscous…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
We show that the atomic force microscope can perform stress relaxation and creep compliance measurements on living cells. We propose a method to obtain the mechanical properties of the studied biomaterial: the relaxation time, the elastic…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
The description of hydrodynamic interactions between a particle and the surrounding liquid, down to the nanometer scale, is of primary importance since confined liquids are ubiquitous in many natural and technological situations. In this…
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule…
Gravitational and hydrodynamical perturbations are analysed in a relativistic plasma containing a mixture of interacting fluids characterized by a non-negligible bulk viscosity coefficient. The energy-momentum transfer between the…
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…
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…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…