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Binary neural networks (BNNs) have demonstrated their ability to solve complex tasks with comparable accuracy as full-precision deep neural networks (DNNs), while also reducing computational power and storage requirements and increasing the…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from \emph{in vivo} single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of…
A novel ultra-long distributed vibration sensing (DVS) system using forward transmission and coherent detection is proposed and experimentally demonstrated. In the proposed scheme, a pair of multi-span optical fibers are deployed for…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
Since their invention in the 1980s [1], optical tweezers have found a wide range of applications, from biophotonics and mechanobiology to microscopy and optomechanics [2, 3, 4, 5]. Simulations of the motion of microscopic particles held by…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
We deduce a fully analytical model to predict the artifacts of the measuring device handles in Single Molecule Force Spectroscopy experiments. As we show, neglecting the effects of the handle stiffness can lead to crucial overestimation or…
This report presents a unified treatment of the density of states for the knots and folds of polymer chains. The physical realization of such systems ranges from DNA molecules to the microscopic configurations of space-time.
Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids in dependence of the molecular weight of the DNA-chains, and the concentration and valence of the surrounding ionic medium. The…
We study the electrical conductance $G$ and the thermopower $S$ of single-molecule junctions, and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping.…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
In many cases, the computing resources are limited without the benefit from GPU, especially in the edge devices of IoT enabled systems. It may not be easy to implement complex AI models in edge devices. The Universal Approximation Theorem…
Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of non-covalent interactions with ligands. Typically, force decreases the lifetimes of intact complexes…
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 the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
A novel non-invasive microscopy technique for imaging and sizing of folded DNA molecules with the use of photovoltaic tweezers and phase-sensitive detection is elaborated and realized. This novel method is compared with the state-of-the-art…