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Biophysics
Published in Walter Fox Smith, Experimental Physics, 2020
Broadly speaking, biophysics is the science of applying physics concepts and tools to investigate problems in biology. Biology is itself a very large field, with topics spanning the molecular scale (as small as 10−9 meters) to entire ecosystems (as large as our own planet, 107 meters). In this section you will be working somewhere in between, at the level of a small organism (10−3 meters), Drosophila melanogaster, also known the common fruit fly. While Drosophila is historically the most widely studied organism in genetics, and thus well-suited for understanding the functions and properties of proteins (molecular level) or neurons (cellular, neural circuit level), here we will focus on the mechanical side of things – that is, the animal’s physical response to stimuli. The key question you will seek to answer: How does an animal use simple “rules” in its movement to accomplish a complicated task?
Biophysical and Biochemical Characterization of Peptide, Protein, and Bioconjugate Products
Published in Sandeep Nema, John D. Ludwig, Parenteral Medications, 2019
Tapan K. Das, James A. Carroll
Biophysical characterization of therapeutic candidates in drug discovery is critical to selection and optimization of protein molecules that have the desired biological activity, and to ensure developability of drug candidates that can be efficiently developed and manufactured. An important first step in characterization is to determine the potential liabilities in the amino acid sequence and other parts (for contents other than amino acid) of the biotherapeutic candidate. These liabilities are often referred to as “hot spots.” There are some amino acids or groups of amino acids that exhibit common occurrences of chemical or physical degradation events such as oxidation and deamidation. For example, the amino acid methionine (Met) undergoes oxidation, especially in the presence of oxygen and when it is on the protein surface exposed to bulk solvent. Similarly, a surface-exposed pair of asparagine–glycine (Asn-Gly) when present in a loosely formed structural domain in the protein may be prone to deamidation under certain formulation conditions [6].
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Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
There are dangers in applying a rate-determining step theory to complex biological processes. First and foremost, the processes and structures are truly intricate and ingenious. Forcing a simplistic analysis prevents the elucidation of details. What is the role of the protein structure in binding rates and equilibrium constant? What prevents O2 from oxidizing Fe in heme myoglobin and hemoglobin? Why is the Fe on the “wrong” side of the heme group before binding? How far does the Fe have to move when O2 or Co binds? Second, while biochemists often need to measure large numbers (hundreds or even tens of thousands) of samples under a wide variety of conditions (temperature, concentrations, mutation-modified proteins) for drug discovery purposes—requiring quick, simple analysis (e.g., rate-determining-step analysis)—the role of the biophysicist is often to examine the data and biomolecules more carefully to learn structural and mechanistic details. In the end, modern computers can often process data using more complex algorithms without requiring significantly more time for the entire drug search or other process.
Fate of enteric viruses during leafy greens (romaine lettuce) production using treated municipal wastewater and AP205 bacteriophage as a surrogate
Published in Journal of Environmental Science and Health, Part A, 2021
Harvey N. Summerlin, Cícero C. Pola, Karthikeyan R. Chamakura, Ry Young, Terry Gentry, Eric S. McLamore, Raghupathy Karthikeyan, Carmen L. Gomes
All isolates in this study were obtained from Dr. Ry Young’s (Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University) culture collection. AP205 (Acinetobacter phage, AP205, NCBI:txid154784) is a single stranded RNA bacteriophage that has a unique protein sequence among all known single stranded RNA phages with similar chemical composition, shape, and size to norovirus and rotavirus.[19] Hence, AP205 was selected as surrogate bacteriophage for an enteric bacterial virus.[19]Acinetobacter baumannii genotype 16 (ATCC 17988) was selected as host bacteria to propagate AP205. A. baumannii is a Gram-negative opportunistic coccobacilli.[20]
Nano electrical discharge machining – the outlook, challenges, and opportunities
Published in Materials and Manufacturing Processes, 2021
Deepak Kumar, Vivek Bajpai, Nirmal Kumar Singh
6.1 Molecular dynamic simulation (MDS): Molecular dynamics simulation is a numerical simulation method to understand the physical trajectory of ions, atoms, and their interactions considering newton’s law of motion. It is one of the best tools to understand the continuum mechanics of any process at the atomic level. Here, the interaction of atoms and ions is occurring for a fixed period which indicates the dynamic behavior of the system (Fig. 24). The method is very effective where thermal and mechanical behavior is concerned at the atomic level. The simulation method is widely used in biochemistry, [235] biophysics, material science, [236] and micromachining, [237–239] etc. Li et al.[240] demonstrated the internal mechanism of nano-EDM at the atomic level through a hybrid simulation model i.e, MD simulation, and a two-temperature model. They reported that the material disintegrates via shrinkage effect which comes into picture due to temperature gradient and inertia of molten material. Shimada et al.[241] applied the MD simulation to study the self-sharpening mechanism of the tungsten tool in single discharge system at the microscopic level.
Study of Full-body Virtual Embodiment Using noninvasive Brain Stimulation and Imaging
Published in International Journal of Human–Computer Interaction, 2021
In this study, we hypothesized that the anodal tDCS over rTPJ would extend the sense of embodiment by increasing neural firing in the area, with the primary effect on the self-recognition. Possible mechanisms range from the increased SoO for the avatar caused by disrupted self-recognition mechanism (by increased rTPJ activity), to the increased SoA, allowing for easier acceptance of the foreign body by means of lower threshold in action self-attribution. As the effects of tDCS can be both stimulation or inhibition of neural communication, observing any effect would greatly help in clarification of the rTPJ stimulation effects on the sense embodiment. (Department of Biochemistry and Molecular Biophysics Thomas Jessell et al., 2000)