Browsing by Subject "Biophysics"
Now showing items 21-40 of 80
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Electrostatic Contributions to the Thermodynamics of Ribonuclease P Protein Folding
(2016)Electrostatic interactions are of fundamental importance in determining the structure and stability of macromolecules. For example, charge-charge interactions modulate the folding and binding of proteins and influence protein ... -
Energy Transduction By Electron Bifurcation
(2021)Electron bifurcation oxidizes a two-electron donor, using the two electrons to reduce high- and low-potential acceptors. Thus, one electron may move thermodynamically uphill, being kinetically coupled to the downhill flow ... -
Enhancing the Hodgkin-Huxley Equations: Simulations Based on the First Publication in the Biophysical Journal.
(Biophys J, 2015-10-06)The experiments in the Cole and Moore article in the first issue of the Biophysical Journal provided the first independent experimental confirmation of the Hodgkin-Huxley (HH) equations. A log-log plot of the K current versus ... -
Evaluating Dose Summation in Gynecological Brachytherapy
(2015)Purpose Gynecological malignancies present challenges in determining an appropri- ate volumetric dose due to the highly variable physiologic activity of the surrounding tissue. Because of the high doses used in brachytherapy, ... -
Experimental and Theoretical Models to Probe Mechanisms of Biological Charge Flow
(2016)Nature is challenged to move charge efficiently over many length scales. From sub-nm to μm distances, electron-transfer proteins orchestrate energy conversion, storage, and release both inside and outside the cell. Uncovering ... -
Experimentally informed bottom-up model of yeast polarity suggests how single cells respond to chemical gradients
(2021)How do single cells—like neutrophils, amoebae, neurons, yeast, etc.—grow or move in a directed fashion in response to spatial chemical gradients? To address this question, we used the mating response in the budding yeast, ... -
Explore Rb/E2F Activation Dynamics to Define the Control Logic of Cell Cycle Entry in Single Cells
(2015)Control of E2F transcription factor activity, regulated by the action of the retinoblastoma tumor suppressor, is critical for determining cell cycle entry and cell proliferation. However, an understanding of the precise ... -
Global Analysis of Protein Folding Thermodynamics for Disease State Characterization and Biomarker Discovery
(2015)Protein biomarkers can facilitate the diagnosis of many diseases such as cancer and they can be important for the development of effective therapeutic interventions. Current large-scale biomarker discovery and disease state ... -
Harnessing Optical Imaging for Assessing Metabolic Reprogramming in Breast Cancer
(2020)According to the World Health Organization, there were over 2 million new breast cancer cases in 2018. This number is projected to steadily increase year after year. American Cancer Society projections for 2020 list the ... -
In vivo visualization of abdominal malignancies with acoustic radiation force elastography.
(Phys Med Biol, 2008-01-07)The utility of acoustic radiation force impulse (ARFI) imaging for real-time visualization of abdominal malignancies was investigated. Nine patients presenting with suspicious masses in the liver (n = 7) or kidney (n = 2) ... -
Investigating Unfolded Proteins by Small-Angle X-Ray Scattering
(2013)A clear description of the unfolded state is important for understanding protein folding/misfolding reactions. In addition to general ensemble-averaged properties, distributional residue-specific information is particularly ... -
Kinetics of Coupled Binding and Conformational Change in Proteins and RNA
(2015)Ligand binding can modulate function of proteins and nucleic acids by changing both the populations of functionally distinct conformational states and the timescales on which they interconvert. For this reason, both thermodynamic ... -
Lateral Diffusion of Receptors at Synapse Influenced by Synapse Geometry and Macromolecular Crowding
(2014)Cells express a variety of proteins on their surface that allows them to sample the world. These proteins are embedded in the plasma membrane, a bilayer of lipids that surrounds the cell. Since the lipid and protein dimensions ... -
Lysine-Specific Demethylase 1A (LSD1/KDM1A): Identification, Characterization, and Biological Implications of an Extended Recognition Interface for Product and Substrate Binding
(2015)The posttranslation modification of histone proteins within the nucleosomes of chromatin plays important roles in the regulation of gene expression in both normal biological and pathobiological processes. These modifications ... -
M6A Reshapes the Folding and Recognition Landscape of RNAs
(2021)Ribonucleic acid (RNA) is a versatile and dynamic biomolecule that serves as an indispensable component in the central dogma of molecular biology. The realization that RNA plays a wide variety of roles in gene expression ... -
Measurements of Conformational Penalties in Nucleic Acids
(2021)Biomolecules are dynamic entities that adopt a variety of conformations in solution. Conformational changes in biomolecules routinely take place when they take part in biochemical processes such as binding and catalysis. ... -
Mechanisms for Inactivation in Piezo Ion Channels
(2017)An organism’s ability to sense mechanical forces is critical for the detection of environmental stimuli as well as the regulation of internal processes necessary for survival. In vertebrates, the molecular mechanisms of ... -
Mechanobiology of the meniscus.
(J Biomech, 2015-06-01)The meniscus plays a critical biomechanical role in the knee, providing load support, joint stability, and congruity. Importantly, growing evidence indicates that the mechanobiologic response of meniscal cells plays a critical ... -
Modeling Microdomain Evolution on Giant Unilamellar Vesicles using a Phase-Field Approach
(2013)The surface of cell membranes can display a high degree of lateral heterogeneity. This non-uniform distribution of constituents is characterized by mobile nanodomain clusters called rafts. Enriched by saturated phospholipids, ... -
Modeling the Effect of Cell Shape on GTPase Signaling in Neurons
(2015)Biological processes such as cell division and synaptic plasticity are regulated by concentration gradients of signaling molecules. A number of biochemical mechanisms can result in intracellular signaling gradients. For ...
