[ { "id": "authors:4cy8x-k8v15", "collection": "authors", "collection_id": "4cy8x-k8v15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170616-133655981", "type": "book_section", "title": "Host-Virus Interaction: From Metagenomics to Single-Cell Genomics", "book_title": "Encyclopedia of Metagenomics", "author": [ { "family_name": "Tadmor", "given_name": "Arbel D.", "clpid": "Tadmor-A-D" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "contributor": [ { "family_name": "Nelson", "given_name": "Karen E.", "clpid": "Nelson-K-E" } ], "abstract": "It is widely appreciated today that viruses are a dominant and critical part of Earth's biosphere. Yet despite the major advances in the study of environmental viruses in most cases, our knowledge of which viruses go with which hosts is meager. In the classic phage isolation technique, known as the plaque assay, a confluent layer of host cells is infected with a low density of viral particles. When a virus infects a cell within this \"lawn\" of host cells, the cell lyses, and new viral particles infect adjacent cells thereby creating a clearing, or plaque, in the lawn. This technique for isolating viruses requires that the host of the virus be culturable. However, given that >99% of microbes on Earth cannot be cultured at this time, the vast majority of phage-host systems cannot be investigated in the laboratory using these classical phage enrichment techniques. Consequently, little is known about the biology of most viruses and their host specificity in the wild.", "doi": "10.1007/978-1-4899-7478-5_792", "isbn": "978-1-4899-7477-8", "publisher": "Springer", "place_of_publication": "New York, NY", "publication_date": "2015-01-04", "pages": "257-265" }, { "id": "authors:v3def-aaj52", "collection": "authors", "collection_id": "v3def-aaj52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110531-101647091", "type": "book_section", "title": "Thermodynamics of Biological Processes", "book_title": "Biothermodynamics. Part D", "author": [ { "family_name": "Garcia", "given_name": "Hernan G.", "clpid": "Garcia-H-G" }, { "family_name": "Kondev", "given_name": "Jane", "clpid": "Kondev-J" }, { "family_name": "Orme", "given_name": "Nigel", "clpid": "Orme-N" }, { "family_name": "Theriot", "given_name": "Julie A.", "clpid": "Theriot-J-A" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "abstract": "There is a long and rich tradition of using ideas from both equilibrium thermodynamics and its microscopic partner theory of equilibrium statistical mechanics. In this chapter, we provide some background on the origins of the seemingly unreasonable effectiveness of ideas from both thermodynamics and statistical mechanics in biology. After making a description of these foundational issues, we turn to a series of case studies primarily focused on binding that are intended to illustrate the broad biological reach of equilibrium thinking in biology. These case studies include ligand-gated ion channels, thermodynamic models of transcription, and recent applications to the problem of bacterial chemotaxis. As part of the description of these case studies, we explore a number of different uses of the famed Monod\u2013Wyman\u2013Changeux (MWC) model as a generic tool for providing a mathematical characterization of two-state systems. These case studies should provide a template for tailoring equilibrium ideas to other problems of biological interest.", "doi": "10.1016/B978-0-12-381268-1.00014-8", "isbn": "9780123860033", "publisher": "Elsevier", "place_of_publication": "Amsterdam", "publication_date": "2011", "pages": "27-59" }, { "id": "authors:qnfz1-ybs36", "collection": "authors", "collection_id": "qnfz1-ybs36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100817-074128416", "type": "book_section", "title": "Calibration of Tethered Particle Motion Experiments", "book_title": "Mathematics of DNA structure, function and interactions", "author": [ { "family_name": "Han", "given_name": "Lin", "clpid": "Han-Lin" }, { "family_name": "Lui", "given_name": "Bertrand H.", "clpid": "Lui-Bertrand-H" }, { "family_name": "Blumberg", "given_name": "Seth", "clpid": "Blumberg-S" }, { "family_name": "Beausang", "given_name": "John F.", "clpid": "Beausang-J-F" }, { "family_name": "Nelson", "given_name": "Philip C.", "clpid": "Nelson-P-C" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "contributor": [ { "family_name": "Benham", "given_name": "Craig John", "clpid": "Benham-C-J" } ], "abstract": "The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA loping and transcription. TPM experiments exploit the Brownian motion of a DNA-tethered bead to probe biologically relevant conformational changes of the tether. In these experiments, a change in the extent of the bead's random motion is used as a reporter of the underlying macromolecular dynamics and is often deemed sufficient for TPM analysis. However, a complete understanding of how the motion depends on the physical properties of the tethered particle complex would permit more quantitative and accurate evaluation of TPM data. For instance, such understanding can help extract details about a looped complex geometry (or multiple coexisting geometries) from TPM data. To better characterize the measurement capabilities of TPM experiments involving DNA tethers, we have carried out a detailed calibration of TPM magnitude as a function of DNA length and particle size. We also explore how experimental parameters such as acquisition time and exposure time affect the apparent motion of the tethered particle. We vary the DNA length from 200 bp to 2.6 kbp and consider particle diameters of 200, 490 and 970 nm. We also present a systematic comparison between measured particle excursions and theoretical expectations, which helps clarify both the experiments and models of DNA conformation.", "doi": "10.1007/978-1-4419-0670-0_6", "isbn": "978-1-4419-0670-0", "publisher": "Springer", "place_of_publication": "New York", "publication_date": "2009", "pages": "123-138" }, { "id": "authors:0mkhs-wz494", "collection": "authors", "collection_id": "0mkhs-wz494", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111102-074723462", "type": "book_section", "title": "Atomistic Simulations of the Motion of an Edge Dislocation in Aluminum Using the Embedded Atom Method", "book_title": "Shock Compression of Condensed Matter 2001", "author": [ { "family_name": "Bhate", "given_name": "N.", "clpid": "Bhate-N" }, { "family_name": "Clifton", "given_name": "R. J.", "clpid": "Clifton-R-J" }, { "family_name": "Phillips", "given_name": "R.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "contributor": [ { "family_name": "Furnish", "given_name": "M .D.", "clpid": "Furnish-M-D" }, { "family_name": "Thadhani", "given_name": "N. N.", "clpid": "Thadhani-N-N" }, { "family_name": "Horie", "given_name": "Y.", "clpid": "Horie-Y" } ], "abstract": "The motion of an edge dislocation is analyzed for temperatures ranging from 10 K to 200 K and for stresses up to 5 GPa. The dislocation velocity versus the applied shear stress curve can be divided into four regimes corresponding to successively higher shear stresses. In the first regime,\nthe applied shear stress is below the Peierls stress and the dislocation velocity is nominally zero. In the second regime, the dislocation velocity decreases with increasing temperature indicating the presence of a drag due to thermal phonons. In the third regime, the dislocation reaches a sub-sonic limiting velocity that can be predicted by a two-dimensional lattice-dynamics analysis. Such an\nanalysis predicts a limiting velocity for a moving defect when the phase velocity and the group velocity are equal. If even higher shear stresses are applied, the dislocation travels with a transonic velocity of \u221a2 times the shear wave speed.", "doi": "10.1063/1.1483548", "isbn": "0-7354-0068-7", "publisher": "American Institute of Physics", "place_of_publication": "Melville, N.Y.", "publication_date": "2002-07-08", "pages": "339-342" }, { "id": "authors:5ck70-j6f85", "collection": "authors", "collection_id": "5ck70-j6f85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171213-092247784", "type": "book_section", "title": "Nanomechanics of Defects in Solids", "book_title": "Advances in Applied Mechanics", "author": [ { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "contributor": [ { "family_name": "van der Giessen", "given_name": "Erik", "clpid": "van-der-Giessen-E" }, { "family_name": "Wu", "given_name": "Theodore Y.", "clpid": "Wu-T-Y-T" } ], "abstract": "This chapter examines different aspects of nanomechanics of defects in solids. The methods by which the classical boundary-value problems of continuum mechanics can be imbued with atomistic content are reviewed. Microscopic modeling is founded on the fundamental assertion that beneath the details of observed macroscopic phenomenology, there is a set of microscopic processes which, when understood, rationalize the observed macroscopic behavior to the extent of enabling quantitative predictions. The microscopic simulation of materials is based on the evolution of degrees of freedom that are governed by the Schrodinger equation. It is found that either phenomenologically, or through explicit calculational strategies, the electronic degrees of freedom is implicitly subsumed in the effective pair potential. Once the pair potential has been identified, it is a straightforward matter to evaluate radial derivatives and the corresponding force fields. The energy associated with each distortion may be computed explicitly by recourse to direct atomistics. The contribution due to slip may be extracted by subtracting off the bulk elastic energy. As a result, the exact misfit energy is determined from atomistics. The cohesive-zone theories applied to fracture are also elaborated.", "doi": "10.1016/S0065-2156(08)70184-4", "isbn": "978-0-12-002036-2", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1998", "pages": "1-79" } ]