A5042482638- Cellular Mechanics and Interactions
- Microtubule and mitosis dynamics
- Neuroscience and Neuropharmacology Research
- Protein Structure and Dynamics
- Genomics and Chromatin Dynamics
- Protein Kinase Regulation and GTPase Signaling
- Bioinformatics and Genomic Networks
- Photoreceptor and optogenetics research
- Thermal properties of materials
- Receptor Mechanisms and Signaling
- Mechanical and Optical Resonators
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Carbon Nanotubes in Composites
- Gene Regulatory Network Analysis
- Postharvest Quality and Shelf Life Management
- Stochastic processes and statistical mechanics
- Molecular Junctions and Nanostructures
- Scientific Computing and Data Management
- Graphene research and applications
- Material Dynamics and Properties
- Chromosomal and Genetic Variations
- Photosynthetic Processes and Mechanisms
- Plant Physiology and Cultivation Studies
- Mathematical Biology Tumor Growth
Monash University
2023
South College
2021
GlaxoSmithKline (United States)
2021
University of Connecticut
2017-2018
Jackson Laboratory
2015-2018
UConn Health
2012-2016
Washington University in St. Louis
2010-2011
University of Washington
2011
University of Pennsylvania
2005-2008
Abstract Simple alkyl FA esters have numerous uses, including serving as biodiesel, a fuel for compression ignition (diesel) engines. The use of acid‐catalyzed esterification the synthesis FAME from acid oil, by‐product edible vegetable oil refining that is produced soapstock, was investigated. Soybean contained 59.3 wt% FFA, 28.0 TAG, 4.4 DAG, and less than 1% MAG. Maximum occurred at 65°C 26 h reaction molar ratio total FA/methanol/sulfuric 1∶15∶1.5. Residual unreacted species under these...
Regulation of actin dynamics through the Nck/N-WASp (neural Wiskott–Aldrich syndrome protein)/Arp2/3 pathway is essential for organogenesis, cell invasiveness, and pathogen infection. Although many proteins involved in this are known, detailed mechanism by which it functions remains undetermined. To examine signaling mechanism, we used a two-pronged strategy involving computational modeling quantitative experimentation. We developed predictions Nck-dependent polymerization using Virtual Cell...
Stress generation by myosin minifilaments is analyzed via simulation of their motion in a random actin network. The stresses are overwhelmingly contractile because minifilament equilibrium positions having stress have lower energy than those for expansive stress. Force chains lead to unexpectedly large stresses.
ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization gene regulation mediated by specific protein factors. Recently, we showed single experiment information at all genomic scales interest, from high-resolution locations binding sites enriched factors, to low resolution nonenriched reflect topological neighborhoods higher-order chromosome folding. This multilevel nature...
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization development, cell differentiation transcriptional regulation.There is now a widespread need for computational tools to generate analyze structural models from 3C data.Here we introduce our GeNOme Modeling Engine (3D-GNOME), web service which generates structures data provides visually inspect annotate resulting structures,...
The optimal pharmacokinetic (PK) required for a drug candidate to elicit efficacy is highly dependent on the targeted pharmacology, relationship that often not well characterized during early phases of discovery. Generic assumptions around PK and potency risk misguiding screening compound design toward nonoptimal absorption, distribution, metabolism, excretion (ADME) or molecular properties ultimately may increase attrition as hit-to-lead lead optimization timelines. present work introduces...
We develop and solve a continuum theory for the piezoelectric response of one dimensional nanotubes nanowires, apply to study electromechanical effects in BN nanotubes. find that polarization nanotube depends on its aspect ratio, dimensionless constant specifying ratio strengths elastic electrostatic interactions. The solutions model as these two parameters are varied discussed. is applied estimate electric potential induced along length uniaxial stress.
The combinatorial explosion produced by the multi-state, multi-subunit character of CaMKII has made analysis and modeling this key signaling protein a significant challenge. Using rule-based particle-based approaches, we construct exact models holoenzyme dynamics study these as function number subunits per holoenzyme, N. Without phosphatases activation are independent structure unless phosphorylation significantly alters kinase activity subunit. With model is size for N > 6. We introduce an...
We use numerical simulations to study the properties of a model lamellipodium as it disassembles by filament severing. The growing is modeled 2D or 3D periodic lattice crosslinked actin filaments. At each time step new layer filaments added at membrane, existing are severed stochastically and disconnected sections network removed. Filament aging including several different chemical states. annealing included allowing grow studied functions number states severing rates. width proportional sum...
We calculate effects of an applied helically symmetric potential on the low energy electronic spectrum a carbon nanotube in continuum approximation. The depends strength this and dimensionless geometrical parameter, $P$, which is ratio circumference to pitch helix. find that minimum band gap semiconducting reduced by arbitrarily weak helical potential, for given field there optimal $P$ produces biggest change gap. For metallic nanotubes Fermi velocity strong fields two small gaps appear at...
Abstract Recent technical and methodological advances have greatly enhanced genome-wide association studies (GWAS). The advent of low-cost, whole-genome sequencing facilitates high-resolution variant identification, the development linear mixed models (LMM) allows improved identification putatively causal variants. While essential for correcting false positive associations due to sample relatedness population stratification, LMMs commonly been restricted quantitative variables. However,...
The effect of dried jackfruit powder on the extrusion cornmeal was investigated for creation a naturally flavored and nutritious expanded snack. Both ripe unripe varying particle size (100–1000 μm) were mixed with corn grits (200–1000 to elucidate macronutrient composition (ripe vs jackfruit), feed parameters. Minimum residence time, specific mechanical energy (SME) product parameters including expansion ratio hardness evaluated twin-screw corotating extruder. Hindrance extrudate observed...
We use a numerical simulation to model an actin comet tail as it grows from the surface of small object (a bead) and disassembles by severing. explore dependence macroscopic properties such local radius length on several controllable properties, namely bead diameter, velocity, severing rate per unit length, gel mesh size. The predicts F-actin density with initial exponential decay followed abrupt at edge tail, that diameter is constant along tail. results are used fit formula relating...
Proteins, especially those involved in signaling pathways are composed of functional modules connected by linker domains with varying degrees flexibility. To understand the structure-function relationships these macromolecules, it is helpful to visualize geometric arrangement domains. Furthermore, accurate spatial representation domain structure necessary for coarse-grain models multi-molecular interactions that comprise pathways.We introduce a new tool, mol2sphere, transforms atomistic...
Table of contents A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis complex structures different...
We develop and solve a continuum theory for the piezoelectric response of nanotubes under applied uniaxial torsional stresses. find that is controlled by chiral angle, aspect ratio, two dimensionless parameters specifying ratio strengths electrostatic elastic energies. The model solved in limiting cases solutions are discussed. These systems found to have several unexpected physical effects not seen conventional bulk systems, including strong stretch-twist coupling development significant...
Australian native fruits are well-adapted to local climate and have growing interest in their nutritional sensory qualities. Among the most highly produced finger limes muntries. However, published literature on characterisation especially processing is limited. Water binding foods linked preservation through amount of water microbes need be active drying energy required. How affects this binding, however, poorly understood. This work studied apples compared with muntries limes. Unlike...
Abstract Summary Proteins, especially those involved in signaling pathways are composed of functional modules consisting long strings amino acids. These “domains” linked together geometric arrangements that can be rigid or flexible, depending on the nature linker domains. To understand structure-function relationships these macromolecules, it would helpful to visualize arrangement Furthermore, accurate spatial representation domain structure is necessary for coarse-grain models...