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Retinal Optical Coherence Tomography (OCT), a noninvasive cross-sectional scan of the eye with qualitative 3D visualization of the retinal anatomy is use to study the retinal structure and the presence of pathogens. The advent of the…
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…
The proper orthogonal decomposition (POD) is a powerful classical tool in fluid mechanics used, for instance, for model reduction and extraction of coherent flow features. However, its applicability to high-resolution data, as produced by…
A novel hybrid Random Forest and Convolutional Neural Network (CNN) framework is presented for oil-water classification in hyperspectral images (HSI). To address the challenge of preserving spatial context, the images were divided into…
We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
Fast slip flow was reported for water inside the interlayer gallery between graphene layers or carbon nanotubes. We report here that this flow rate enhancement (over two orders) breaks down with the presence of chemical functionalization…
The local structure of liquid water as a function of temperature is a source of intense research. This structure is intimately linked to the dynamics of water molecules, which can be measured using Raman and infrared spectroscopies. The…
The enormous diversity of life forms thriving in drastically different environmental milieus involves a complex interplay among constituent proteins interacting with each other. However, the organizational principles characterizing the…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Identifying Out-of-distribution (OOD) data is becoming increasingly critical as the real-world applications of deep learning methods expand. Post-hoc methods modify softmax scores fine-tuned on outlier data or leverage intermediate feature…
Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…
Robust semantic segmentation of intraoperative image data could pave the way for automatic surgical scene understanding and autonomous robotic surgery. Geometric domain shifts, however, although common in real-world open surgeries due to…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
Face representation in the wild is extremely hard due to the large scale face variations. To this end, some deep convolutional neural networks (CNNs) have been developed to learn discriminative feature by designing properly margin-based…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well…