Publications by authors named "Sudip Roy"

Background: Many healthcare systems have implemented intensive outpatient primary care programs with the hopes of reducing healthcare costs.

Objective: The Veterans Health Administration (VHA) piloted primary care intensive management (PIM) for patients at high risk for hospitalization or death, or "high-risk." We evaluated whether a referral model would decrease high-risk patient costs.

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Pancreatic lipase (PL) is a keen target for anti-obesity therapy that reduces dietary fat absorption. Here, we investigated the binding patterns of 220 PL inhibitors having experimental IC values, using molecular docking and binding energy calculations. Screening of these compounds illustrated most of them bound at the catalytic site (S1-S2 channel) and a few compounds are at the non-catalytic site (S2-S3 channel/S1-S3 channel) of PL.

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Introduction: Lichen planus (LP) is a relatively common chronic, mucocutaneous disease of autoimmune origin, involves oral mucosa, skin, scalp, nails, and genital mucosa. The prevalence of oral LP (OLP) varies worldwide, commonly seen in middle-aged and elderly people. It usually presents as symmetrical and bilateral or multiple lesions with burning sensation (BS) sometimes accompanied by pain.

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Intensive management programs may improve health care experiences among high-risk and complex patients. We assessed patient experience among (1) prior enrollees (n = 59) of an intensive management program (2014-2018); (2) nonenrollees (n = 356) at program sites; and (3) nonprogram site patients (n = 728), using a patient survey based on the Consumer Assessment of Healthcare Providers and Systems in 2019. Outcomes included patient ratings of patient-centered care; overall health care experience; and satisfaction with their usual outpatient care provider.

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The emergence of pandemic situations originated from severe acute respiratory syndrome (SARS)-CoV-2 and its new variants created worldwide medical emergencies. Due to the non-availability of efficient drugs and vaccines at these emergency hours, repurposing existing drugs can effectively treat patients critically infected by SARS-CoV-2. Finding a suitable repurposing drug with inhibitory efficacy to a host-protein is challenging.

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Since the onset of global pandemic, the most focused research currently in progress is the development of potential drug candidates and clinical trials of existing FDA approved drugs for other relevant diseases, in order to repurpose them for the COVID-19. At the same time, several high throughput screenings of drugs have been reported to inhibit the viral components during the early course of infection but with little proven efficacies. Here, we investigate the drug repurposing strategies to counteract the coronavirus infection which involves several potential targetable host proteins involved in viral replication and disease progression.

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In recent times, computational methods played an important role in the down selection of chemical compounds, which could be a potential drug candidate with a high affinity to target proteins. However, the screening methodologies, including docking, often fails to identify the most effective compound, which could be a ligand for the target protein. To solve that, here we have integrated meta-dynamics, an enhanced sampling molecular simulation method, with all-atom molecular dynamics to determine a specific compound that could target the main protease of novel severe acute respiratory syndrome coronavirus 2 (SARS-COV-2).

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Among recent technological advances, microfluidic biochips have been leading a prominent solution for healthcare and miniaturized bio-laboratories with the assurance of high sensitivity and reconfigurability. On increasing more unreliable communication networks day-by-day, technological shifts in the fields of communication and security are now converging. In today's cyber threat landscape, these microfluidic biochips are ripe targets of powerful cyber-attacks from different hackers or cyber-criminals.

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Antibody-drug conjugates (ADCs) combine the high specificity of antibodies with cytotoxic payloads. However, the present strategies for the synthesis of ADCs either yield unstable or heterogeneous products or involve complex processes. Here, we report a computational approach that leverages molecular docking and molecular dynamics simulations to design ADCs that self-assemble through the non-covalent binding of the antibody to a payload that we designed to act as an affinity ligand for specific conserved amino acid residues in the antibody.

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Pt-water interfaces have been of immense interest in the field of energy storage and conversion. Studying this interface using both experimental and theoretical tools is challenging. On the theoretical front, typically one uses classical molecular dynamics (MD) simulations to handle large system sizes or time scales while for a more accurate quantum mechanical description Born Oppenheimer MD (BOMD) is typically used.

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Breast cancer is the most devastating disease among females globally. Conventional chemotherapeutic regimen relies on the use of highly cytotoxic drugs as monotherapy and combination therapy leading to severe side effects to the patients as collateral damage. Moreover, combining hydrophobic and hydrophilic drugs create erratic biodistribution and suboptimal medicinal outcome.

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In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution.

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The molecular thermodynamics and kinetics of CO sorption in Polyethylenimine (PEI) melt have been investigated systematically using GCMC and MD simulations. We elucidate presence of significant structural and dynamic heterogeneity associated with the overall absorption process. CO adsorption in a PEI membrane shows a distinct two-stage process of a rapid CO adsorption at the interfaces (hundreds of picoseconds) followed by a significantly slower diffusion limited release toward the interior bulk regions of PEI melt (hundreds of nanoseconds to microseconds).

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Perfluoropolyether tetraol (PFPE tetraol) possesses a hydrophobic perfluoropolyether chain in the backbone and two hydroxyl groups at each chain terminal, which facilitates the formation of hydrogen bonds with water molecules resulting in the formation an extended physical network. About 3 wt% water was required for the formation of the microphase separated physical network of PFPE tetraol. The mechanism responsible for the microphase separation of water clusters in the physical network was studied using a combination of techniques such as NMR spectroscopy, molecular dynamics (MD) simulations and DSC.

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We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations.

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Background: Philadelphia chromosome, a hallmark of chronic myeloid leukemia (CML), plays a key role in disease pathogenesis. It reflects a balanced reciprocal translocation between long arms of chromosomes 9 and 22 involving and genes, respectively. An accurate and reliable detection of fusion gene is necessary for the diagnosis and monitoring of CML.

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Calcifying odontogenic cyst (COC) is a term used broadly to define lesions which were either cystic/solid in nature. However, a new term defining dentinogenic ghost cell tumor (DGCT), as its neoplastic counterpart, histopathologically showed the presence of dentinoid-like areas, ghost cells and ameloblastomatous-like odontogenic epithelium. This possesses a great challenge to an oral pathologist in diagnosing and differentiating it from solid multicystic ameloblastoma or COCs so as to ensure the biological behavior and pathogenesis behind its multifaceted nature.

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Herein, we study the permeation free energy of bare and octane-thiol-capped gold nanoparticles (AuNPs) translocating through a lipid membrane. To investigate this, we have pulled the bare and capped AuNPs from bulk water to the membrane interior and estimated the free energy cost. The adsorption of the bare AuNP on the bilayer surface is energetically favorable but further loading inside it requires energy.

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In the chemical world, evolution is mirrored in the origin of nanoscale supramolecular structures from molecular subunits. The complexity of function acquired in a supramolecular system over a molecular subunit can be harnessed in the treatment of cancer. However, the design of supramolecular nanostructures is hindered by a limited atomistic level understanding of interactions between building blocks.

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Covalent organic nanosheets (CONs) have emerged as functional two-dimensional materials for versatile applications. Although π-π stacking between layers, hydrolytic instability, possible restacking prevents their exfoliation on to few thin layered CONs from crystalline porous polymers. We anticipated rational designing of a structure by intrinsic ionic linker could be the solution to produce self-exfoliated CONs without external stimuli.

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Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common.

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Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations.

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Microsecond atomic-scale molecular dynamics simulation has been employed to calculate the glass-transition temperature (Tg) of cis- and trans-1,4-polybutadiene (PB) and 1,4-polyisoprene (PI). Both all-atomistic and united-atom models have been simulated using force fields, already available in literature. The accuracy of these decade old force fields has been tested by comparing calculated glass-transition temperatures to the corresponding experimental values.

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