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At least 469 records · Page 26

Integrative teaching of metabolic modeling and flux analysis with interactive python modules

Abstract The modeling of rates of biochemical reactions—fluxes—in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint‐based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to‐date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C‐metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands‐on computer laboratory component of a four‐day metabolic modeling workshop and participant survey results showed improvements in learners' self‐assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.

Kaste, Joshua A. M.↗

Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference—Advancing Biological and Pharmaceutical Mass Spectrometry

Following the highly successful Chinese American Society for Mass Spectrometry (CASMS) conferences in the previous 2 years, the 3rd CASMS Conference was held virtually on August 28–31, 2023, using the Gather. Town platform to bring together scientists in the MS field. The conference offered a 4-day agenda with a scientific program consisting of two plenary lectures, and 14 parallel symposia in which a total of 70 speakers presented technological innovations and their applications in proteomics and biological MS and metabo-lipidomics and pharmaceutical MS. In addition, 16 invited speakers/panelists presented at two research-focused and three career development workshops. Moreover, 86 posters, 12 lightning talks, 3 sponsored workshops, and 11 exhibitions were presented, from which 9 poster awards and 2 lightning talk awards were selected. Furthermore, the conference featured four young investigator awardees to highlight early-career achievements in MS from our society. In conclusion, the conference provided a unique scientific platform for young scientists (i.e. graduate students, postdocs, and junior faculty/investigators) to present their research, meet with prominent scientists, learn about career development, and job opportunities (http://casms.org).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Nonperturbative Topological Phenomena in QCD and Related Theories

Here, this book introduces a variety of aspects in nonperturbative Quantum Chromodynamics (QCD), focusing on the topological objects present in gauge theories. These objects, like magnetic monopoles, instantons, instanton-dyons, sphalerons, QCD flux tubes, etc, are first introduced individually and, later, treated collectively. As ensembles, they produce various phenomena that can be modeled numerically in lattice gauge theories and such collective effects, produced on the lattice, are extensively discussed in some chapters. In turn, the notion of duality, which is crucial in modern field/string theories, is elucidated by taking into consideration the electric-magnetic duality, the Poisson duality, and the AdS/CFT duality.This monograph is based on various lectures given by Edward Shuryak at Stony Brook during the last three decades and it is meant for advanced graduate students and young researchers in theoretical and mathematical physics who are willing to consolidate their knowledge in the topological phenomena encountered in fundamental QCD research.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Strongly Interacting Matter Under Rotation: An Introduction

Ultrarelativistic collisions between heavy nuclei briefly generate the quark-gluon plasma (QGP), a new state of matter characterized by deconfined par- tons last seen microseconds after the Big Bang. The properties of the QGP are of intense interest, and a large community has developed over several decades, to pro- duce, measure and understand this primordial plasma. The plasma is now recog- nized to be a strongly-coupled fluid with remarkable properties, and hydrodynamics is commonly used to quantify and model the system. An important feature of any fluid is its vorticity, related to the local angular momentum density; however, this degree of freedom has received relatively little attention because no experimental signals of vorticity had been detected. Thanks to recent high-statistics datasets from experiments with precision tracking and complete kinemetic coverage at collider energies, hyperon spin polarization measurements have begun to uncover the vor- ticity of the QGP created at the Relativistic Heavy Ion Collider. The injection of this new degree of freedom into a relatively mature field of research represents an enormous opportunity to generate new insights into the physics of the QGP. The community has responded with enthusiasm, and this book (to be published as a volume of Lecture Notes in Physics series by Springer) represents some of the diverse lines of inquiry into aspects of strongly interacting matter under rotation

Becattini, Francesco↗

Computational Nuclear Physics and Post Hartree-Fock Methods

We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions on strategies for porting the code to present and planned high-performance computing facilities.

Lietz, Justin↗

Hermite analogs of the lowest order Raviart–Thomas mixed method for convection–diffusion equations

The Raviart–Thomas mixed finite-element method of the lowest order (Raviart and Thomas in mixed finite-element methods for second-order elliptic problems, Lecture Notes in mathematics, Springer, New York, 1977) commonly known as the RT{sub 0} method, is a well-established and popular numerical tool to solve diffusion-like problems providing flux continuity across inter-element boundaries. Douglas and Roberts extended the method to the case of more general second-order boundary-value problems including the convection–diffusion equations (cf. this journal Douglas in Comput Appl Math 1:91–103; 1982). The main drawback of these methods, however, is the poor representation of the primal variable by piecewise constant functions. The Hermite analog of the RT{sub 0} method for treating pure diffusion phenomena proposed in Ruas (J Comput Appl Math, 246:234–242; 2013) proved to be a valid alternative to attain higher order approximation of the primal variable while keeping intact the matrix structure and the quality of the discrete flux variable of the original RT{sub 0} method. Non-trivial extensions of this method are studied here that can be viewed as Hermite analogs of the two Douglas and Roberts’ versions of the RT{sub 0} method, to solve convection–diffusion equations. A detailed convergence study is carried out for one of the Hermite methods, and numerical results illustrate the performance of both of them, as compared to each other and to the corresponding mixed methods.

97 MATHEMATICS AND COMPUTING↗

A practical introduction to tensor networks: Matrix product states and projected entangled pair states

This is a partly non-technical introduction to selected topics on tensor network methods, based on several lectures and introductory seminars given on the subject. It should be a good place for newcomers to get familiarized with some of the key ideas in the field, specially regarding the numerics. After a very general introduction we motivate the concept of tensor network and provide several examples. We then move on to explain some basics about Matrix Product States (MPS) and Projected Entangled Pair States (PEPS). Selected details on some of the associated numerical methods for 1d and 2d quantum lattice systems are also discussed. - Highlights: • A practical introduction to selected aspects of tensor network methods is presented. • We provide analytical examples of MPS and 2d PEPS. • We provide basic aspects on several numerical methods for MPS and 2d PEPS. • We discuss a number of applications of tensor network methods from a broad perspective.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Foreward

This special issue of Computers & Chemical Engineering contains extended versions of selected contributions from the 8th International Conference on the Foundations of Computer-Aided Process Design (FOCAPD-2014), held at the Suncadia Resort in Cle Elum, Washington, USA, July 13–17, 2014. These papers were recommended by the International Programming Committee and constitute a representative sample of the invited plenary lectures,future perspectives, and contributed papers.

99 GENERAL AND MISCELLANEOUS↗

Creating a ‘Collaboratory’ environment to transcend traditional research barriers: Insights from the United States

Today’s scientific endeavors often resemble a large lecture hall partitioned into separate sectors. Scientists, engineers and students study big questions largely in isolation. Here, local factors drive their activities, but the groups have overlapping interests and capabilities for tackling big questions about our planet’s energy future.

99 GENERAL AND MISCELLANEOUS↗

Radiation Oncology Medical Student Clerkship: Implementation and Evaluation of a Bi-institutional Pilot Curriculum

Purpose: To develop and evaluate a structured didactic curriculum to complement clinical experiences during radiation oncology clerkships at 2 academic medical centers. Methods and Materials: A structured didactic curriculum was developed to teach fundamentals of radiation oncology and improve confidence in clinical competence. Curriculum lectures included: (1) an overview of radiation oncology (history, types of treatments, and basic clinic flow); (2) fundamentals of radiation biology and physics; and (3) practical aspects of radiation treatment simulation and planning. In addition, a hands-on dosimetry session taught students fundamentals of treatment planning. The curriculum was implemented at 2 academic departments in 2012. Students completed anonymous evaluations using a Likert scale to rate the usefulness of curriculum components (1 = not at all, 5 = extremely). Likert scores are reported as (median [interquartile range]). Results: Eighteen students completed the curriculum during their 4-week rotation (University of Chicago n=13, Harvard Longwood Campus n=5). All curriculum components were rated as extremely useful: introduction to radiation oncology (5 [4-5]); radiation biology and physics (5 [5-5]); practical aspects of radiation oncology (5 [4-5]); and the treatment planning session (5 [5-5]). Students rated the curriculum as “quite useful” to “extremely useful” (1) to help students understand radiation oncology as a specialty; (2) to increase student comfort with their specialty decision; and (3) to help students with their future transition to a radiation oncology residency. Conclusions: A standardized curriculum for medical students completing a 4-week radiation oncology clerkship was successfully implemented at 2 institutions. The curriculum was favorably reviewed. As a result of completing the curriculum, medical students felt more comfortable with their specialty decision and better prepared to begin radiation oncology residency.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Microscopy & Microanalysis 2019 in Portland, Oregon

The Microscopy Society of America (MSA), the Microanalysis Society (MAS), and the International Field Emission Society (IFES) cordially invite you to Microscopy & Microanalysis 2019 in Portland, Oregon. We are excited and honored to feature two Nobel Prize laureates as our plenary lecturers. Our first plenary speaker will be Dr. Joachim Frank, Professor of Biochemistry and Molecular Biophysics and of Biological Sciences at Columbia University, New York. He shared with Jacques Dubochet and Richard Henderson the 2017 Nobel Prize in Chemistry for “Developing cryo-electron microscopy for the high resolution structure determination of biomolecules in solution.” Our second plenary speaker will be Dr. Richard Henderson of the Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge, UK. He will present a talk titled “Single particle cryoEM: potential for further improvement.” As usual, M&M 2019 will present a great variety of symposia topics in analytical, life, and physical sciences. This year, we have a special symposium: “Cryo-EM – from Physics to Cell Biology: Honoring the Remarkable Legacy of Ken Downing.” It will showcase the late Dr. Downing’s work in single-particle cryo-EM, cryo-electron tomography, and the microscopy methods he used for his seminal discoveries. Preceding the M&M 2019 technical program, we will have two pre-meeting congresses. Education and training are important components of the M&M technical program each year, and 2019 is no exception. Six Sunday short courses on material science, biology, and data analysis will be presented. Additional opportunities are available in tutorials in biology and physical sciences during the meeting week. Finally, our popular microscopy outreach workshop “Project MICRO” will be in the MegaBooth all week. For a complete description of the technical program and educational opportunities, please go to http://www.microscopy.org/MandM/2019. The Call for Papers and other aspects of the program and the meeting are provided under “Scientific Program.” The Executive Program Committee welcomes you to Portland for an excellent and compelling Microscopy & Microanalysis 2019. Catch up with old friends and make new ones! Look for opportunities to attend society business meetings and socials during the week. On behalf of MSA, MAS, IFES, in cooperation with over a hundred symposia organizers and countless volunteers, we look forward to seeing you in Portland this August!

Microscopy, microanalysis↗

Nanotechnology: Colourful Particles for Spectrometry

In 1857 Michael Faraday gave a well-attended lecture at the Royal Institution of Great Britain, in which he presented his pioneering experimental work that investigated the interaction of light with matter. Faraday’s study probed the fundamental properties of light as it was reflected and absorbed by progressively smaller particles. Very fine gold particles dispersed in liquid were shown to produce vivid colors not seen in larger particles. Faraday did not know he had created colloidal suspensions of quantum dots, but his insight correctly concluded that the distinct colors were somehow due to the minute size of the gold particles. This great experimental physicist had actually glimpsed a special condition where the particle’s quantum nature was expressed. This work set the future course for nanoscience and quantum theory, but it would take another 125 years before the physical basis of this phenomenon would be explained by quantum size effects. It is now known that when quantum dots are exposed to UV light, some of the electrons are excited as they gain energy, however they remain confined to discrete energy levels not observed in larger particles and solid materials. When the electrons relax and lose their energy, the quantum dot emits light at a specific color that varies with the size of the quantum dot. Bao and Bawendi have cleverly exploited the unique optical properties intrinsic to colloidal quantum dots to develop an innovative compact optical spectrometer that could be integrated with a smart phone camera or as a versatile miniature handheld sensing tool.

Colloidal quantum dots↗

Foreword to Special Issue: Papers from the 54th Annual Meeting of the APS Division of Plasma Physics, Providence, Rhode Island, USA, 2012

Each year, the annual meeting of the APS Division of Plasma Physics (DPP) brings together a broad representation of the many active subfields of plasma physics and enjoys an audience that is equally diverse. The meeting was well attended and largely went as planned despite the interventions of hurricane Sandy which caused the city of Providence to shut-down during the first day of the conference. The meeting began on Monday morning with a review of the physics of cosmic rays, 2012 being the 100th year since their discovery, which illustrated the central importance of plasma physics to astrophysical problems. Subsequent reviews covered the importance of tokamak plasma boundaries, progress towards ignition on the National Ignition Facility (NIF), and magnetized plasma turbulence. The Maxwell prize address, by Professor Liu Chen, covered the field of nonlinear Alfvén wave physics. Tutorial lectures were presented on the verification of gyrokinetics, new capabilities in laboratory astrophysics, magnetic flux compression, and tokamak plasma start-up.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The fundamental role of symmetry in nuclear models

The purpose of these lectures is to illustrate how symmetry and pattern recognition play essential roles in the progression from experimental observation to an understanding of nuclear phenomena in terms of interacting neutrons and protons. We do not discuss weak interactions nor relativistic and sub-nucleon degrees of freedom. The explicit use of symmetry and the power of algebraic methods, in combination with analytical and geometrical methods are illustrated by their use in deriving a shell-model description of nuclear rotational dynamics and the structure of deformed nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Supersymmetric quantum mechanics and Painlevé equations

In these lecture notes we shall study first the supersymmetric quantum mechanics (SUSY QM), specially when applied to the harmonic and radial oscillators. In addition, we will define the polynomial Heisenberg algebras (PHA), and we will study the general systems ruled by them: for zero and first order we obtain the harmonic and radial oscillators, respectively; for second and third order the potential is determined by solutions to Painlevé IV (PIV) and Painlevé V (PV) equations. Taking advantage of this connection, later on we will find solutions to PIV and PV equations expressed in terms of confluent hypergeometric functions. Furthermore, we will classify them into several solution hierarchies, according to the specific special functions they are connected with.

97 MATHEMATICS AND COMPUTING↗

Non abelian hydrodynamics and heavy ion collisions

The goal of the relativistic heavy ion collisions (RHIC) program is to create a state of matter where color degrees of freedom are deconfined. The dynamics of matter in this state, in spite of the complexities of quantum chromodynamics, is largely determined by the conservation laws of energy momentum and color currents. Therefore it is possible to describe its main features in hydrodynamic terms, the very short color neutralization time notwithstanding. In this lecture we shall give a simple derivation of the hydrodynamics of a color charged fluid, by generalizing the usual derivation of hydrodynamics from kinetic theory to the non abelian case.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Primordial nucleosynthesis: A cosmological point of view

Primordial nucleosynthesis remains as one of the pillars of modern cosmology. It is the test-ing ground upon which all cosmological models must ultimately rest. It is our only probe of the universe during the first few minutes of cosmic expansion and in particular during the important radiation-dominated epoch. These lectures review the basic equations of space-time, cosmology, and big bang nucleosynthesis. We will then review the current state of observational constraints on primordial abundances along with the key nuclear reactions and their uncertainties. We summarize which nuclear measure-ments are most crucial during the big bang. We also review various cosmological models and their constraints. In particular, we summarize the constraints that big bang nucleosynthesis places upon the possible time variation of fundamental constants, along with constraints on the nature and origin of dark matter and dark energy, long-lived supersymmetric particles, gravity waves, and the primordial magnetic field.

79 ASTRONOMY AND ASTROPHYSICS↗