A5031585022- Protein Structure and Dynamics
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Quantum Dots Synthesis And Properties
- Fluid Dynamics and Mixing
- Advanced Proteomics Techniques and Applications
- Perovskite Materials and Applications
- Advanced Battery Technologies Research
- Genomics and Phylogenetic Studies
- Carbon Nanotubes in Composites
- Advancements in Battery Materials
- Nanopore and Nanochannel Transport Studies
- Innovative Microfluidic and Catalytic Techniques Innovation
- Algal biology and biofuel production
- Conducting polymers and applications
- Bioinformatics and Genomic Networks
- Machine Learning in Materials Science
- Photochemistry and Electron Transfer Studies
- Mechanical and Optical Resonators
- Aerogels and thermal insulation
- Graphene research and applications
- Solar-Powered Water Purification Methods
- Low-power high-performance VLSI design
- Material Dynamics and Properties
- Microbial Community Ecology and Physiology
University of Michigan
2013-2021
Washington State University
2012-2017
Penn State Milton S. Hershey Medical Center
2013
Memorial University of Newfoundland
2013
Eastern Health
2013
Memorial Sloan Kettering Cancer Center
2013
Henry Ford Health System
2013
Shinshu University Hospital
2013
Kyoto University Hospital
2013
South Dakota State University
2011-2012
Abstract We report the results of two fully automated structure prediction pipelines, “Zhang‐Server” and “QUARK”, in CASP13. The pipelines were built upon C‐I‐TASSER C‐QUARK programs, which turn are based on I‐TASSER QUARK but with three new modules: (a) a novel multiple sequence alignment (MSA) generation protocol to construct deep sequence‐profiles for contact prediction; (b) an improved meta‐method, NeBcon, combines predictors, including ResPRE that predicts contact‐maps by coupling...
The success of genome sequencing techniques has resulted in rapid explosion protein sequences. Collections multiple homologous sequences can provide critical information to the modeling structure and function unknown proteins. There are however no standard efficient pipeline available for sensitive sequence alignment (MSA) collection. This is particularly challenging when large whole-genome metagenome databases involved.We developed DeepMSA, a new open-source method MSA construction, which...
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER QUARK pipelines for template-based modeling (TBM) free (FM), test them in the CASP12 experiment. The combination of successfully folds three medium-size FM targets that have more than 150 residues, even though interplay between still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance quality models, particularly targets, new pipelines....
Abstract Sequence-based contact prediction has shown considerable promise in assisting non-homologous structure modeling, but it often requires many homologous sequences and a sufficient number of correct contacts to achieve folds. Here, we developed method, C-QUARK, that integrates multiple deep-learning coevolution-based contact-maps guide the replica-exchange Monte Carlo fragment assembly simulations. The method was tested on 247 non-redundant proteins, where C-QUARK could fold 75% cases...
Recent CASP experiments have witnessed exciting progress on folding large-size non-humongous proteins with the assistance of co-evolution based contact predictions. The success is however anecdotal due to requirement prediction methods for high volume sequence homologs that are not available most protein targets. Development efficient can generate balanced and reliable maps different type targets essential enhance rate ab initio structure prediction.We developed a new pipeline, NeBcon, which...
Understanding the structure of aqueous electrolytes at interfaces is essential for predicting and optimizing device performance a wide variety emerging energy environmental technologies. In this work, we investigate two common salt solutions, NaCl KCl, hydrophobic interface within narrow carbon nanotubes (CNTs). Using combination first-principles classical molecular dynamics simulations in conjunction with orbital analysis, find that solvation cations CNTs can deviate substantially from...
Accurate prediction of atomic-level protein structure is important for annotating the biological functions molecules and designing new compounds to regulate functions. Template-based modeling (TBM), which aims construct structural models by copying refining frameworks other known proteins, remains most accurate method prediction. Due difficulty in recognizing distant-homology templates, however, accuracy TBM decreases rapidly when evolutionary relationship between query template vanishes. In...
Abstract Introduction The ocean microbiome represents one of the largest microbiomes and produces nearly half primary energy on planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications oceanic metagenomes for protein structure function prediction. Results By processing 1.3 TB high-quality reads from Tara Oceans data, obtain 97 million non-redundant genes. Of 5721 Pfam families that lack experimental structures, 2801 have at least...
The molecular interactions between solvent and nanoparticles during photoactive layer formation in organic photovoltaic (OPV) cells influence the morphology of hence determine power conversion efficiency. Prediction optimal synthesis parameters OPVs, such as choice solvent, processing temperature, nanoparticle concentration, requires fundamental understanding mechanisms that govern agglomeration solvents. In this study, we used dynamics simulations to simulate a commonly nanoparticle,...
Recent studies suggest that electron transport layers (ETLs) comprising [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), employed in planar perovskite solar cells, reduce hysteresis by passivating the deep trap states, thereby underscoring importance of interfacial structures. To gain physical insights into PCBM–perovskite interfaces during solution processing, we performed molecular dynamics simulations PCBMs solvated chlorobenzene near (110) and (100) surfaces. Our results indicate...
This research study investigates bubble and liquid circulation patterns in a vertical column photobioreactor (PBR) both experimentally as well computationally using computational fluid dynamics (CFD). Dispersed gas-liquid flow the rectangular PBR are modeled Eulerian-Lagrangian approach. A low Reynolds number k-epsilon CFD model is used to describe pattern near wall. flat surface achieve sufficient light penetration into system. Bubble size distribution measurements were completed high-speed...
This research project investigates bubble and liquid circulation patterns in a vertical column photobioreactor (PBR) both experimentally as well computationally using Computational Fluid Dynamics (CFD). Dispersed gas–liquid flow the rectangular PBR are modeled Eulerian–Lagrangian approach. A low Reynolds number k–ε CFD model is used to describe pattern near wall. Bubble size distribution measurements carried out high-speed digital camera. flat surface achieve sufficient light penetration...
We present a multiscale model, based on molecular dynamics (MD) and kinetic Monte Carlo (kMC), to study the aggregation driven growth of colloidal particles. Coarse-grained (CGMD) simulations are employed detect key agglomeration events calculate corresponding rate constants. The kMC employ these constants in stochastic framework track agglomerates over longer time scales length scales. One hallmarks model is unique methodology characterize events. accounts for individual cluster-scale...
The goal of this research is to investigate heat transfer effects two phase gas-liquid flows in a column photobioreactor (PBR) experimentally as well computationally using Computational Fluid Dynamics (CFD). authors have completed preliminary study on bubble formation, rise and resulting circulation patterns lab-scale experiments CFD simulations. This extends previous work by investigating the relationships drag coefficient Reynolds number with superficial gas velocity within PBR. It...
Solution-processed deposition of carbon nanotubes (CNTs) provides a cost-effective means to synthesize uniform vertically or horizontally aligned nanostructures on top substrates. The efficacy depends the solubility CNTs in solvent as well ordering relative These governing factors, which determine specific morphologies that are deposited, determined by molecular interactions between and substrate molecules. In an effort mimic conditions during solution-processed substrates, we employed...
This article presents a review of recent modelling work on various aspects thin-film photovoltaic solar cells. Organic cells and perovskite are chosen as representative systems. The critical issues for these technologies, which include improving the efficiency, developing cost-effective sustainable manufacturing methods identifying earth-abundant materials, discussed. Modelling studies, mostly based first principles electronic structure calculations all-atom coarse-grained molecular...
Today’s Li-ion technology is highly optimized for performance at relatively slow charging operation. However, significant challenges still present fast conditions (> 4C). These include large kinetic polarizations, concentration gradients, heat generation, and Li metal plating on the surface. In state-of-the-art batteries with high energy densities, electrodes are thick 100 μm), which leads to a tradeoff between density high-power performance. This because thicker tortuous pathway...
Self-assembly of carbon nanotubes (CNTs) on silicon substrates has myriad applications including nanotube based electrochemical energy conversion and storage devices, such as batteries super-capacitors. Patterned assembly CNTs is required in order to control the effective electrical conductivity mechanical properties these devices achieve substantial improvement their performance. Solution-based self-assembly provides a cost-effective means synthesize uniform vertically or horizontally...