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Open Access Publications from the University of California

Department of Physics

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The Physics Department at UC San Diego is home to approximately 65 faculty members whose research interests include astrophysics, biophysics, condensed-matter physics, high-energy particle physics, and plasma physics. The graduate program is home to about 160 PhD students in training. In addition to accommodating about 400 physics majors, course enrollments total 16,000 students each academic year, mostly in introductory and general education courses.

Department of Physics

There are 1611 publications in this collection, published between 1979 and 2024.
Open Access Policy Deposits (1600)

Characterizing dry mass and volume changes in human multiple myeloma cells upon treatment with proteotoxic and genotoxic drugs.

Multiple myeloma (MM) is a cancer of terminally differentiated plasma cells. MM remains incurable, but overall survival of patients has progressively increased over the past two decades largely due to novel agents such as proteasome inhibitors (PI) and the immunomodulatory agents. While these therapies are highly effective, MM patients can be de novo resistant and acquired resistance with prolonged treatment is inevitable. There is growing interest in early, accurate identification of responsive versus non-responsive patients; however, limited sample availability and need for rapid assays are limiting factors. Here, we test dry mass and volume as label-free biomarkers to monitor early response of MM cells to treatment with bortezomib, doxorubicin, and ultraviolet light. For the dry mass measurement, we use two types of phase-sensitive optical microscopy techniques: digital holographic tomography and computationally enhanced quantitative phase microscopy. We show that human MM cell lines (RPMI8226, MM.1S, KMS20, and AMO1) increase dry mass upon bortezomib treatment. This dry mass increase after bortezomib treatment occurs as early as 1 h for sensitive cells and 4 h for all tested cells. We further confirm this observation using primary multiple myeloma cells derived from patients and show that a correlation exists between increase in dry mass and sensitivity to bortezomib, supporting the use of dry mass as a biomarker. The volume measurement using Coulter counter shows a more complex behavior; RPMI8226 cells increase the volume at an early stage of apoptosis, but MM.1S cells show the volume decrease typically observed with apoptotic cells. Altogether, this cell study presents complex kinetics of dry mass and volume at an early stage of apoptosis, which may serve as a basis for the detection and treatment of MM cells.

Measurement of electroweak production of a W boson in association with two jets in proton–proton collisions at s=13Te

A measurement is presented of electroweak (EW) production of a W boson in association with two jets in proton-proton collisions at s=13Te . The data sample was recorded by the CMS Collaboration at the LHC and corresponds to an integrated luminosity of 35.9 fb-1 . The measurement is performed for the ℓν jj final state (with ℓν indicating a lepton-neutrino pair, and j representing the quarks produced in the hard interaction) in a kinematic region defined by invariant mass mjj>120Ge and transverse momenta pTj>25Ge . The cross section of the process is measured in the electron and muon channels yielding σEW(Wjj)=6.23±0.12(stat)±0.61(syst)pb per channel, in agreement with leading-order standard model predictions. The additional hadronic activity of events in a signal-enriched region is studied, and the measurements are compared with predictions. The final state is also used to perform a search for anomalous trilinear gauge couplings. Limits on anomalous trilinear gauge couplings associated with dimension-six operators are given in the framework of an effective field theory. The corresponding 95% confidence level intervals are -2.3

Control of Bacillus subtilis Replication Initiation during Physiological Transitions and Perturbations

Bacillus subtilis and Escherichia coli are evolutionarily divergent model organisms whose analysis has enabled elucidation of fundamental differences between Gram-positive and Gram-negative bacteria, respectively. Despite their differences in cell cycle control at the molecular level, the two organisms follow the same phenomenological principle, known as the adder principle, for cell size homeostasis. We thus asked to what extent B. subtilis and E. coli share common physiological principles in coordinating growth and the cell cycle. We measured physiological parameters of B. subtilis under various steady-state growth conditions with and without translation inhibition at both the population and single-cell levels. These experiments revealed core physiological principles shared between B. subtilis and E. coli Specifically, both organisms maintain an invariant cell size per replication origin at initiation, under all steady-state conditions, and even during nutrient shifts at the single-cell level. Furthermore, the two organisms also inherit the same "hierarchy" of physiological parameters. On the basis of these findings, we suggest that the basic principles of coordination between growth and the cell cycle in bacteria may have been established early in evolutionary history.IMPORTANCE High-throughput, quantitative approaches have enabled the discovery of fundamental principles describing bacterial physiology. These principles provide a foundation for predicting the behavior of biological systems, a widely held aspiration. However, these approaches are often exclusively applied to the best-known model organism, E. coli In this report, we investigate to what extent quantitative principles discovered in Gram-negative E. coli are applicable to Gram-positive B. subtilis We found that these two extremely divergent bacterial species employ deeply similar strategies in order to coordinate growth, cell size, and the cell cycle. These similarities mean that the quantitative physiological principles described here can likely provide a beachhead for others who wish to understand additional, less-studied prokaryotes.

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