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Parallel kinematic manipulators (PKM) are characterized by closed kinematic loops, due to the parallel arrangement of limbs but also due to the existence of kinematic loops within the limbs. Moreover, many PKM are built with limbs…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers. The ability to precisely predict protein thermostability is…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
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…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
Cellular contractility, migration, and extracellular matrix (ECM) mechanics are critical for a wide range of biological processes including embryonic development, wound healing, tissue morphogenesis, and regeneration. Even though the…
Protein-protein interactions are central mediators in many biological processes. Accurately predicting the effects of mutations on interactions is crucial for guiding the modulation of these interactions, thereby playing a significant role…
The optical properties of phase-change materials (PCM) can be tuned to multiple levels by controlling the transition between their amorphous and crystalline phases. In multi-material PCM structures, the number of discrete reflectance levels…
To design molecular spin qubits with enhanced quantum coherence, a control of the coupling between the local vibrations and the spin states is crucial, which could be realized in principle by engineering molecular structures via…
Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM…
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
While nucleic-acids can be readily amplified for single-marker detection, a comparable method for proteins assay is currently unavailable. Proteins potentiometric detections at 10-20 molar have been demonstrated, but the mechanism remains…
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal…
Programmable and reconfigurable optics hold significant potential for transforming a broad spectrum of applications, spanning space explorations to biomedical imaging, gas sensing, and optical cloaking. The ability to adjust the optical…
The analysis of stress response systems in microorganisms can reveal molecular strategies for regulatory control and adaptation. Here, we focus on the Cad module, a subsystem of E. coli's response to acidic stress, which is conditionally…
Projection neurons in the dorsal horn relay nociceptive input to supraspinal centers. During central sensitization, a subset of them switches from tonic firing to plateau potentials with sustained afterdischarges, a change that requires…
It is known that curvature relation plays a key role in the propagation of two-dimensional waves in an excitable model. Such a relation is believed to obey the eikonal equation for typical excitable models (e.g., the FitzHugh-Nagumo (FHN)…
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…