Search Results - "DILL, KEN A."

The Protein-Folding Problem, 50 Years On by Dill, Ken A., MacCallum, Justin L.

“…The protein-folding problem was first posed about one half-century ago. The term refers to three broad questions: (i) What is the physical code by which an…”
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Bacterial growth laws reflect the evolutionary importance of energy efficiency by Maitra, Arijit, Dill, Ken A.

“…We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model…”
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Protein evolution speed depends on its stability and abundance and on chaperone concentrations by Agozzino, Luca, Dill, Ken A.

“…Proteins evolve at different rates. What drives the speed of protein sequence changes? Two main factors are a protein’s folding stability and aggregation…”
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Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference by MacCallum, Justin L., Perez, Alberto, Dill, Ken A.

“…More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often,…”
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Physical limits of cells and proteomes by Dill, Ken A, Ghosh, Kingshuk, Schmit, Jeremy D

“…What are the physical limits to cell behavior? Often, the physical limitations can be dominated by the proteome, the cell’s complement of proteins. We combine…”
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Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects by Rocklin, Gabriel J, Mobley, David L, Dill, Ken A, Hünenberger, Philippe H

“…The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the…”
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Accelerating molecular simulations of proteins using Bayesian inference on weak information by Perez, Alberto, MacCallum, Justin L., Dill, Ken A.

“…Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid…”
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Molecular Motors: Power Strokes Outperform Brownian Ratchets by Wagoner, Jason A, Dill, Ken A

“…Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Their actions are often described in terms of…”
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Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines by Wagoner, Jason A, Dill, Ken A

“…Abstract Many biomolecular machines need to be both fast and efficient. How has evolution optimized these machines along the tradeoff between speed and…”
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Protein aggregation in salt solutions by Kastelic, Miha, Kalyuzhnyi, Yurij V., Hribar-Lee, Barbara, Dill, Ken A., Vlachy, Vojko

“…Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible…”
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The protein folding problem by Dill, Ken A, Ozkan, S Banu, Shell, M Scott, Weikl, Thomas R

“…The "protein folding problem" consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict…”
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Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers by Guseva, Elizaveta, Zuckermann, Ronald N., Dill, Ken A.

“…It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain…”
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Diet modulates brain network stability, a biomarker for brain aging, in young adults by Mujica-Parodi, Lilianne R., Amgalan, Anar, Sultan, Syed Fahad, Antal, Botond, Sun, Xiaofei, Skiena, Steven, Lithen, Andrew, Adra, Noor, Ratai, Eva-Maria, Weistuch, Corey, Govindarajan, Sindhuja Tirumalai, Strey, Helmut H., Dill, Ken A., Stufflebeam, Steven M., Veech, Richard L., Clarke, Kieran

“…Epidemiological studies suggest that insulin resistance accelerates progression of age-based cognitive impairment, which neuroimaging has linked to brain…”
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In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability by Sharma, Vikas K., Patapoff, Thomas W., Kabakoff, Bruce, Pai, Satyan, Hilario, Eric, Zhang, Boyan, Li, Charlene, Borisov, Oleg, Kelley, Robert F., Chorny, Ilya, Zhou, Joe Z., Dill, Ken A., Swartz, Trevor E.

“…For mAbs to be viable therapeutics, they must be formulated to have low viscosity, be chemically stable, and have normal in vivo clearance rates. We explored…”
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General Mechanism of Two-State Protein Folding Kinetics by Rollins, Geoffrey C, Dill, Ken A

“…We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which…”
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Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics by Chodera, John D, Singhal, Nina, Pande, Vijay S, Dill, Ken A, Swope, William C

“…To meet the challenge of modeling the conformational dynamics of biological macromolecules over long time scales, much recent effort has been devoted to…”
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Review of the application of Kirchhoff's Laws of series and parallel flows to pharmacology: Defining organ clearance by Pachter, Jonathan Asher, Dill, Ken A., Sodhi, Jasleen K., Benet, Leslie Z.

“…Dosing rate decisions for drugs and changes in dosing in a patient due to disease states, drug interactions and pharmacogenomics are all based on clearance, a…”
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Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes by Dixit, Purushottam D, Jain, Abhinav, Stock, Gerhard, Dill, Ken A

“…We are interested inferring rate processes on networks. In particular, given a network’s topology, the stationary populations on its nodes, and a few global…”
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Computing protein stabilities from their chain lengths by Ghosh, Kingshuk, Dill, Ken A

“…New amino acid sequences of proteins are being learned at a rapid rate, thanks to modern genomics. The native structures and functions of those proteins can…”
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Highly Charged Proteins: The Achilles' Heel of Aging Proteomes by de Graff, Adam M.R., Hazoglou, Michael J., Dill, Ken A.

“…As cells and organisms age, their proteins sustain increasing amounts of oxidative damage. It is estimated that half of all proteins are damaged in old…”
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