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The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…
The claustrum (Cl) is a thin grey matter structure located in the center of each brain hemisphere. Cl has been hypothesized as a central hub of the brain for multisensory/sensorimotor integration, consciousness, and attention. Accumulating…
Strong gravitational lensing of gravitational wave sources offers a novel probe of both the lens galaxy and the binary source population. In particular, the strong lensing event rate and the time delay distribution of multiply-imaged…
The intensity matching approach for tractable performance evaluation and optimization of cellular networks is introduced. It assumes that the base stations are modeled as points of a Poisson point process and leverages stochastic geometry…
Access to high-energy particle beams is key for testing high-energy physics (HEP) instruments. Accelerators for cancer treatment can serve as such a testing ground. However, HEP instrument tests typically require particle fluxes…
Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response,…
As one of the probes of universe, strong gravitational lensing systems allow us to compare different cosmological models and constrain vital cosmological parameters. This purpose can be reached from the dynamic and geometry properties of…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new…
The mechanical properties of the cell depend crucially on the tension of its cytoskeleton, a biopolymer network that is put under stress by active motor proteins. While the fibrous nature of the network is known to strongly affect the…
Current medical image analysis systems are typically task-specific, requiring separate models for classification and segmentation, and lack the flexibility to support user-defined workflows. To address these challenges, we introduce…
The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the…
A computer-aided detection (CAD) system for the identification of pulmonary nodules in low-dose multi-detector helical Computed Tomography (CT) images with 1.25 mm slice thickness is presented. The basic modules of our lung-CAD system, a…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
Medical image analysis is central to drug discovery and preclinical evaluation, where scalable, objective readouts can accelerate decision-making. We address classification of paclitaxel (Taxol) exposure from phase-contrast microscopy of C6…
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller…
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…
Glaucoma is the second driving reason for partial or complete blindness among all the visual deficiencies which mainly occurs because of excessive pressure in the eye due to anxiety or depression which damages the optic nerve and creates…