Network science of biological systems at different scales: A review

NASA Astrophysics Data System (ADS)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

NASA Astrophysics Data System (ADS)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

End-Directedness and Context in Nonliving Dissipative Systems

NASA Astrophysics Data System (ADS)

Dixon, James A.; Kay, Bruce A.; Davis, Tehran J.; Kondepudi, Dilip

Biological organisms are distinguished from non-living systems, in part, by their ability to choose and strive towards particular ends. This end-directed behavior is seen across all five biological kingdoms, from single-celled organisms to the most advanced primates. The ubiquitous nature of end-directedness, across such a wide variety of biological entities, suggests that a deeper principle may be at work. We propose that end-directedness, rather than being a special ability of living systems, is actually a fundamental property of a larger class of physical systems, called dissipative structures, which are formed and maintained by the flow of energy and matter. Our work shows that dissipative structures "behave so as to persist", seeking states that increase their rate of entropy production, and thus facilitate their own persistence. In addition, we suggest that biological entities create their exquisite sensitivity to context by interweaving this fundamental end-directedness with the contextual and physical constraints of their environments. The result is a repertoire of complex behavior. We provide an example of such complex behavior emerging from contextual and physical constraints coupled with end-directedness.

Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

Treesearch

Bruce E. Rieman; Jason B. Dunham; James L. Clayton

2006-01-01

Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions....

Biological and nonbiological complex drugs for multiple sclerosis in Latin America: regulations and risk management.

PubMed

Carrá, Adriana; Macías Islas, Miguel Angel; Tarulla, Adriana; Bichuetti, Denis Bernardi; Finkelsztejn, Alessandro; Fragoso, Yara Dadalti; Árcega-Revilla, Raul; Cárcamo Rodríguez, Claudia; Durán, Juan Carlos; Bonitto, Juan García; León, Rosalba; Oehninger Gatti, Carlos; Orozco, Geraldine; Vizcarra Escobar, Darwin

2015-06-01

Biological drugs and nonbiological complex drugs with expired patents are followed by biosimilars and follow-on drugs that are supposedly similar and comparable with the reference product in terms of quality, safety and efficacy. Unlike simple molecules that can be copied and reproduced, biosimilars and follow-on complex drugs are heterogeneous and need specific regulations from health and pharmacovigilance agencies. A panel of 14 Latin American experts on multiple sclerosis from nine different countries met to discuss the recommendations regarding biosimilars and follow-on complex drugs for treating multiple sclerosis. Specific measures relating to manufacturing, therapeutic equivalence assessment and pharmacovigilance reports need to be implemented before commercialization. Physical, chemical, biological and immunogenic characterizations of the new product need to be available before clinical trials start. The new product must maintain the same immunogenicity as the original. Automatic substitution of biological and complex drugs poses unacceptable risks to the patient.

Bringing the physical sciences into your cell biology research

PubMed Central

Robinson, Douglas N.; Iglesias, Pablo A.

2012-01-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences. PMID:23112230

Bringing the physical sciences into your cell biology research.

PubMed

Robinson, Douglas N; Iglesias, Pablo A

2012-11-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences.

Complex, Dynamic Combination of Physical, Chemical and Nutritional Variables Controls Spatio-Temporal Variation of Sandy Beach Community Structure

PubMed Central

Ortega Cisneros, Kelly; Smit, Albertus J.; Laudien, Jürgen; Schoeman, David S.

2011-01-01

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right. PMID:21858213

Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

PubMed

Ortega Cisneros, Kelly; Smit, Albertus J; Laudien, Jürgen; Schoeman, David S

2011-01-01

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right.

Bio-Physics Manifesto -- for the Future of Physics and Biology

NASA Astrophysics Data System (ADS)

Oono, Y.

2008-04-01

The Newtonian revolution taught us how to dissect phenomena into contingencies (e.g., initial conditions) and fundamental laws (e.g., equations of motion). Since then, `fundamental physics' has been pursuing purer and leaner fundamental laws. Consequently, to explain real phenomena a lot of auxiliary conditions become required. Isn't it now the time to start studying `auxiliary conditions' seriously? The study of biological systems has a possibility of shedding light on this neglected side of phenomena in physics, because we organisms were constructed by our parents who supplied indispensable auxiliary conditions; we never self-organize. Thus, studying the systems lacking self-organizing capability (such as complex systems) may indicate new directions to physics and biology (biophysics). There have been attempts to construct a `general theoretical framework' of biology, but most of them never seriously looked at the actual biological world. Every serious natural science must start with establishing a phenomenological framework. Therefore, this must be the main part of bio-physics. However, this article is addressed mainly to theoretical physicists and discusses only certain theoretical aspects (with real illustrative examples).

Perspectives on theory at the interface of physics and biology.

PubMed

Bialek, William

2018-01-01

Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. I am an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.

Perspectives on theory at the interface of physics and biology

NASA Astrophysics Data System (ADS)

Bialek, William

2018-01-01

Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. I am an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.

Physical and biological mechanisms of nanosecond- and microsecond-pulsed FE-DBD plasma interaction with biological objects

NASA Astrophysics Data System (ADS)

Dobrynin, Danil

2013-09-01

Mechanisms of plasma interaction with living tissues and cells can be quite complex, owing to the complexity of both the plasma and the tissue. Thus, unification of all the mechanisms under one umbrella might not be possible. Here, analysis of interaction of floating electrode dielectric barrier discharge (FE-DBD) with living tissues and cells is presented and biological and physical mechanisms are discussed. In physical mechanisms, charged species are identified as the major contributors to the desired effect and a mechanism of this interaction is proposed. Biological mechanisms are also addressed and a hypothesis of plasma selectivity and its effects is offered. Spatially uniform nanosecond and sub-nanosecond short-pulsed dielectric barrier discharge plasmas are gaining popularity in biological and medical applications due to their increased uniformity, lower plasma temperature, lower surface power density, and higher concentration of the active species produced. In this presentation we will compare microsecond pulsed plasmas with nanosecond driven systems and their applications in biology and medicine with specific focus on wound healing and tissue regeneration. Transition from negative to positive streamer will be discussed with proposed hypothesis of uniformity mechanisms of positive streamer and the reduced dependence on morphology and surface chemistry of the second electrode (human body) being treated. Uniform plasma offers a more uniform delivery of active species to the tissue/surface being treated thus leading to better control over the biological results.

Physical Therapy in the Treatment of Central Pain Mechanisms for Female Sexual Pain.

PubMed

Vandyken, Carolyn; Hilton, Sandra

2017-01-01

The complexity of female sexual pain requires an interdisciplinary approach. Physical therapists trained in pelvic health conditions are well positioned to be active members of an interdisciplinary team addressing the assessment and treatment of female sexual pain. Changes within physical therapy practice in the last ten years have resulted in significant utilization of pelvic floor muscle relaxation and manual therapy techniques to address a variety of pelvic pain conditions, including female sexual pain. However, sexual pain is a complex issue giving credence to the necessity of addressing all of the drivers of the pain experience- biological, psychological and social. This review aims to reconcile current pain science with a plan for integrating a biopsychosocial approach into the evaluation and subsequent treatment for female sexual pain for physical therapists. A literature review of the important components of skilled physical therapy interventions is presented including the physical examination, pain biology education, cognitive behavioral influences in treatment design, motivational interviewing as an adjunct to empathetic practice, and the integration of non-threatening movement and mindfulness into treatment. A single case study is used to demonstrate the biopsychosocial framework utilized in this approach. Appropriate measures for assessing psychosocial factors are readily available and inform a reasoned approach for physical therapy design that addresses both peripheral and central pain mechanisms. Decades of research support the integration of a biopsychosocial approach in the treatment of complex pain, including female sexual pain. It is reasonable for physical therapists to utilize evidence based strategies such as CBT, pain biology education, Mindfulness Based Stress Reduction (MBSR), yoga and imagery based exercises to address the biopsychosocial components of female sexual pain. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

The Physics of Life and Quantum Complex Matter: A Case of Cross-Fertilization

PubMed Central

Poccia, Nicola; Bianconi, Antonio

2011-01-01

Progress in the science of complexity, from the Big Bang to the coming of humankind, from chemistry and biology to geosciences and medicine, and from materials engineering to energy sciences, is leading to a shift of paradigm in the physical sciences. The focus is on the understanding of the non-equilibrium process in fine tuned systems. Quantum complex materials such as high temperature superconductors and living matter are both non-equilibrium and fine tuned systems. These topics have been subbjects of scientific discussion in the Rome Symposium on the “Quantum Physics of Living Matter”. PMID:26791661

Complex systems: physics beyond physics

NASA Astrophysics Data System (ADS)

Holovatch, Yurij; Kenna, Ralph; Thurner, Stefan

2017-03-01

Complex systems are characterised by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behaviour. Examples arise both in the physical and non-physical worlds. The study of complex systems forms a new interdisciplinary research area that cuts across physics, biology, ecology, economics, sociology, and the humanities. In this paper we review the essence of complex systems from a physicists' point of view, and try to clarify what makes them conceptually different from systems that are traditionally studied in physics. Our goal is to demonstrate how the dynamics of such systems may be conceptualised in quantitative and predictive terms by extending notions from statistical physics and how they can often be captured in a framework of co-evolving multiplex network structures. We mention three areas of complex-systems science that are currently studied extensively, the science of cities, dynamics of societies, and the representation of texts as evolutionary objects. We discuss why these areas form complex systems in the above sense. We argue that there exists plenty of new ground for physicists to explore and that methodical and conceptual progress is needed most.

Kinetics and Photochemistry of Ruthenium Bisbipyridine Diacetonitrile Complexes: An Interdisciplinary Inorganic and Physical Chemistry Laboratory Exercise.

PubMed

Rapp, Teresa L; Phillips, Susan R; Dmochowski, Ivan J

2016-12-13

The study of ruthenium polypyridyl complexes can be widely applied across disciplines in the undergraduate curriculum. Ruthenium photochemistry has advanced many fields including dye-sensitized solar cells, photoredox catalysis, light-driven water oxidation, and biological electron transfer. Equally promising are ruthenium polypyridyl complexes that provide a sterically bulky, photolabile moiety for transiently "caging" biologically active molecules. Photouncaging involves the use of visible (1-photon) or near-IR (2-photon) light to break one or more bonds between ruthenium and coordinated ligand(s), which can occur on short time scales and in high quantum yields. In this work we demonstrate the use of a model "caged" acetonitrile complex, Ru(2,2'-bipyridine) 2 (acetonitrile) 2 , or RuMeCN in an advanced synthesis and physical chemistry laboratory. Students made RuMeCN in an advanced synthesis laboratory course and performed UV-vis spectroscopy and electrochemistry. The following semester students investigated RuMeCN photolysis kinetics in a physical chemistry laboratory. These two exercises may also be combined to create a 2-week module in an advanced undergraduate laboratory course.

Kinetics and Photochemistry of Ruthenium Bisbipyridine Diacetonitrile Complexes: An Interdisciplinary Inorganic and Physical Chemistry Laboratory Exercise

PubMed Central

2016-01-01

The study of ruthenium polypyridyl complexes can be widely applied across disciplines in the undergraduate curriculum. Ruthenium photochemistry has advanced many fields including dye-sensitized solar cells, photoredox catalysis, light-driven water oxidation, and biological electron transfer. Equally promising are ruthenium polypyridyl complexes that provide a sterically bulky, photolabile moiety for transiently “caging” biologically active molecules. Photouncaging involves the use of visible (1-photon) or near-IR (2-photon) light to break one or more bonds between ruthenium and coordinated ligand(s), which can occur on short time scales and in high quantum yields. In this work we demonstrate the use of a model “caged” acetonitrile complex, Ru(2,2′-bipyridine)2(acetonitrile)2, or RuMeCN in an advanced synthesis and physical chemistry laboratory. Students made RuMeCN in an advanced synthesis laboratory course and performed UV–vis spectroscopy and electrochemistry. The following semester students investigated RuMeCN photolysis kinetics in a physical chemistry laboratory. These two exercises may also be combined to create a 2-week module in an advanced undergraduate laboratory course. PMID:28649139

A transformative model for undergraduate quantitative biology education.

PubMed

Usher, David C; Driscoll, Tobin A; Dhurjati, Prasad; Pelesko, John A; Rossi, Louis F; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B

2010-01-01

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions.

A Transformative Model for Undergraduate Quantitative Biology Education

PubMed Central

Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

2010-01-01

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions. PMID:20810949

Review Article: Shallow Draughts--Larsen-Freeman and Cameron on Complexity

ERIC Educational Resources Information Center

Gregg, Kevin R.

2010-01-01

Complexity theory is a field of physics that studies the nature and behavior of complex systems, systems whose elements interact in complex and unpredictable ways. Recent years have seen a number of attempts to extend its scope to the biological and social sciences, and now Larsen-Freeman and Cameron offer a view of applied linguistics from a…

Physics met biology, and the consequence was...

PubMed

McLeish, Tom

2011-06-01

We summarise the contributions to the discussion and the links between them. The complex relationship between the physical and biological sciences demonstrates three "axes of tension": the role of simulation, the interplay between levels of explanation, and the generality of "laws". We identify examples of true synergy between approaches that genuinely explore new research territory, and underscore the contemporary value of the type of discussions contained in this volume. Copyright © 2011. Published by Elsevier Ltd.

Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes*

PubMed Central

Stengel, Florian; Aebersold, Ruedi; Robinson, Carol V.

2012-01-01

Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies. PMID:22180098

Simulating Life

ERIC Educational Resources Information Center

Sinclair, Michael; Dauerty, Helene; Alber, Mark

2016-01-01

Biomodeling is the study of the structures and behaviors of interacting biological entities such as molecules, cells, or organisms. While physical and chemical processes give rise to various spatial and temporal structures, even the simplest biological phenomenon is infinitely more complex (Kling 2004). Over the past decade, much of biomodeling…

Chemistry and biological activity of platinum amidine complexes.

PubMed

Michelin, Rino A; Sgarbossa, Paolo; Sbovata, Silvia Mazzega; Gandin, Valentina; Marzano, Cristina; Bertani, Roberta

2011-07-04

Platinum amidine complexes represent a new class of potential antitumor drugs that contain the imino moiety HN=C(sp(2)) bonded to the platinum center. They can be related to the iminoether derivatives, which were recently shown to be the first Pt(II) compounds with a trans configuration endowed with anticancer activity. The chemical and biological properties of platinum amidine complexes, and more generally of platinum imino derivatives, can be rationally modified through suitable synthetic procedures with the aim of improving their cytotoxicity and antitumor activity. The addition of protic nucleophiles to nitriles coordinated to platinum in various oxidation states can offer a wide variety of complexes with chemical, structural, and physical properties specifically tuned for a more efficacious biological response. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Search for organising principles: understanding in systems biology.

PubMed

Mesarovic, M D; Sreenath, S N; Keene, J D

2004-06-01

Due in large measure to the explosive progress in molecular biology, biology has become arguably the most exciting scientific field. The first half of the 21st century is sometimes referred to as the 'era of biology', analogous to the first half of the 20th century, which was considered to be the 'era of physics'. Yet, biology is facing a crisis--or is it an opportunity--reminiscent of the state of biology in pre-double-helix time. The principal challenge facing systems biology is complexity. According to Hood, 'Systems biology defines and analyses the interrelationships of all of the elements in a functioning system in order to understand how the system works.' With 30000+ genes in the human genome the study of all relationships simultaneously becomes a formidably complex problem. Hanahan and Weinberg raised the question as to whether progress will consist of 'adding further layers of complexity to a scientific literature that is already complex almost beyond measure' or whether the progress will lead to a 'science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' At the core of the challenge is the need for a new approach, a shift from reductionism to a holistic perspective. However, more than just a pronouncement of a new approach is needed. We suggest that what is needed is to provide a conceptual framework for systems biology research. We propose that the concept of a complex system, i.e. a system of systems as defined in mathematical general systems theory (MGST), is central to provide such a framework. We further argue that for a deeper understanding in systems biology investigations should go beyond building numerical mathematical or computer models--important as they are. Biological phenomena cannot be predicted with the level of numerical precision as in classical physics. Explanations in terms of how the categories of systems are organised to function in ever changing conditions are more revealing. Non-numerical mathematical tools are appropriate for the task. Such a categorical perspective led us to propose that the core of understanding in systems biology depends on the search for organising principles rather than solely on construction of predictive descriptions (i.e. models) that exactly outline the evolution of systems in space and time. The search for organising principles requires an identification/discovery of new concepts and hypotheses. Some of them, such as coordination motifs for transcriptional regulatory networks and bounded autonomy of levccels in a hierarchy, are outlined in this article. Experimental designs are outlined to help verify the applicability of the interaction balance principle of coordination to transcriptional and posttranscriptional networks.

A mathematical applications into the cells.

PubMed

Tiwari, Manjul

2012-01-01

Biology has become the new "physics" of mathematics, one of the areas of greatest mathematical applications. In turn, mathematics has provided powerful tools and metaphors to approach the astonishing complexity of biological systems. This has allowed the development of sound theoretical frameworks. Here, in this review article, some of the most significant contributions of mathematics to biology, ranging from population genetics, to developmental biology, and to networks of species interactions are summarized.

When physics and biology meet: the nanoscale case.

PubMed

Bueno, Otávio

2011-06-01

As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure (DNA) to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them by microscopic imaging, the different styles of reasoning involved, and the various theoretical, methodological, and axiological differences. I conclude by arguing that, except for the probe microscopes that are used, there is very little in common between the two cases. At the nanoscale, physics and molecular biology seem to meet in a non-unified way. Copyright © 2010 Elsevier Ltd. All rights reserved.

Biological Nature of Knowledge in the Learning Organisation

ERIC Educational Resources Information Center

Hall, William P.

2005-01-01

Purpose: To develop a biological approach to the analysis of learning organisations based on complexity theory, autopoiesis, and evolutionary epistemology. Design/methodology/approach: This paper synthesises ideas from disciplines ranging from physics, epistemology and philosophy of science to military affairs, to sketch a scientific framework in…

Physics through the 1990s: Scientific interfaces and technological applications

NASA Technical Reports Server (NTRS)

1986-01-01

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

Herbal medicine, radical scavenger and metal detoxification: bioinorganic, complexity and nano science perspectives

NASA Astrophysics Data System (ADS)

Sumitro, Sutiman B.; Alit, Sukmaningsih

2018-03-01

Developing Complexity Science and Nano Biological perspective giving the ideas of interfacing between modern physical and biological sciences for more comprehensive understanding of life. The study of bioinorganic is a trans-disciplinary, and will initiate the way to more comprehensive and better understanding life. We can talk about energy generation, motive forces and energy transfer at the level of macromolecules. We can then develop understanding biological behavior on nano size biological materials and its higher order using modern physics as well as thermodynamic law. This is a necessity to ovoid partial understanding of life that are not match with holism. In animal tissues, the accumulation or overwhelmed production of free radicals can damage cells and are believed to accelerate the progression of cancer, cardiovascular disease, and age-related diseases. Thus a guarded balance of radical species is imperative. Edward Kosower [1] proposed an idea of biradical in an aromatic organic compounds. Each of which having unpaired electrons. The magnetic force of this compound used for making agregation based on their magnetic characters. Bioinorganic low molecular weight complex compounds composing herbal medicine can bind toxic metals. This low molecular weight complex molecules then easily excerted the metals from the body, removing them from their either intracellular or extracellular existences. This bioinorganic chelation potential is now inspiring a new therapeutic strategies.

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

Physical biology of human brain development.

PubMed

Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

2015-01-01

Neurodevelopment is a complex, dynamic process that involves a precisely orchestrated sequence of genetic, environmental, biochemical, and physical events. Developmental biology and genetics have shaped our understanding of the molecular and cellular mechanisms during neurodevelopment. Recent studies suggest that physical forces play a central role in translating these cellular mechanisms into the complex surface morphology of the human brain. However, the precise impact of neuronal differentiation, migration, and connection on the physical forces during cortical folding remains unknown. Here we review the cellular mechanisms of neurodevelopment with a view toward surface morphogenesis, pattern selection, and evolution of shape. We revisit cortical folding as the instability problem of constrained differential growth in a multi-layered system. To identify the contributing factors of differential growth, we map out the timeline of neurodevelopment in humans and highlight the cellular events associated with extreme radial and tangential expansion. We demonstrate how computational modeling of differential growth can bridge the scales-from phenomena on the cellular level toward form and function on the organ level-to make quantitative, personalized predictions. Physics-based models can quantify cortical stresses, identify critical folding conditions, rationalize pattern selection, and predict gyral wavelengths and gyrification indices. We illustrate that physical forces can explain cortical malformations as emergent properties of developmental disorders. Combining biology and physics holds promise to advance our understanding of human brain development and enable early diagnostics of cortical malformations with the ultimate goal to improve treatment of neurodevelopmental disorders including epilepsy, autism spectrum disorders, and schizophrenia.

Fundamental Physics Program and the NASA Mission

NASA Technical Reports Server (NTRS)

Trinh, Eugene

2003-01-01

The accomplishments of Physics, the increasing power of its instruments, and its expanding reach into other sciences have generated an unprecedented set of scientific opportunities. The committee has identified six such Grand Challenges listed below in no particular order: Developing quantum technologies. Creating new materials. Understanding complex systems. Unifying the forces of Nature. Exploring the universe Applying Physics to Biology.

Econophysics: from Game Theory and Information Theory to Quantum Mechanics

NASA Astrophysics Data System (ADS)

Jimenez, Edward; Moya, Douglas

2005-03-01

Rationality is the universal invariant among human behavior, universe physical laws and ordered and complex biological systems. Econophysics isboth the use of physical concepts in Finance and Economics, and the use of Information Economics in Physics. In special, we will show that it is possible to obtain the Quantum Mechanics principles using Information and Game Theory.

Hydrology or biology? Modeling simplistic physical constraints on lake carbon biogeochemistry to identify when and where biology is likely to matter

NASA Astrophysics Data System (ADS)

Jones, S.; Zwart, J. A.; Solomon, C.; Kelly, P. T.

2017-12-01

Current efforts to scale lake carbon biogeochemistry rely heavily on empirical observations and rarely consider physical or biological inter-lake heterogeneity that is likely to regulate terrestrial dissolved organic carbon (tDOC) decomposition in lakes. This may in part result from a traditional focus of lake ecologists on in-lake biological processes OR physical-chemical pattern across lake regions, rather than on process AND pattern across scales. To explore the relative importance of local biological processes and physical processes driven by lake hydrologic setting, we created a simple, analytical model of tDOC decomposition in lakes that focuses on the regulating roles of lake size and catchment hydrologic export. Our simplistic model can generally recreate patterns consistent with both local- and regional-scale patterns in tDOC concentration and decomposition. We also see that variation in lake hydrologic setting, including the importance of evaporation as a hydrologic export, generates significant, emergent variation in tDOC decomposition at a given hydrologic residence time, and creates patterns that have been historically attributed to variation in tDOC quality. Comparing predictions of this `biologically null model' to field observations and more biologically complex models could indicate when and where biology is likely to matter most.

Physics Meets Biology (LBNL Summer Lecture Series)

ScienceCinema

Chu, Steven

2018-05-09

Summer Lecture Series 2006: If scientists could take advantage of the awesomely complex and beautiful functioning of biology's natural molecular machines, their potential for application in many disciplines would be incalculable. Nobel Laureate and Director of the Lawrence Berkeley National Laboratory Steve Chu explores Possible solutions to global warming and its consequences.

Fast Quantum Algorithm for Predicting Descriptive Statistics of Stochastic Processes

NASA Technical Reports Server (NTRS)

Williams Colin P.

1999-01-01

Stochastic processes are used as a modeling tool in several sub-fields of physics, biology, and finance. Analytic understanding of the long term behavior of such processes is only tractable for very simple types of stochastic processes such as Markovian processes. However, in real world applications more complex stochastic processes often arise. In physics, the complicating factor might be nonlinearities; in biology it might be memory effects; and in finance is might be the non-random intentional behavior of participants in a market. In the absence of analytic insight, one is forced to understand these more complex stochastic processes via numerical simulation techniques. In this paper we present a quantum algorithm for performing such simulations. In particular, we show how a quantum algorithm can predict arbitrary descriptive statistics (moments) of N-step stochastic processes in just O(square root of N) time. That is, the quantum complexity is the square root of the classical complexity for performing such simulations. This is a significant speedup in comparison to the current state of the art.

Designing and testing a classroom curriculum to teach preschoolers about the biology of physical activity: The respiration system as an underlying biological causal mechanism

NASA Astrophysics Data System (ADS)

Ewing, Tracy S.

The present study examined young children's understanding of respiration and oxygen as a source of vital energy underlying physical activity. Specifically, the purpose of the study was to explore whether a coherent biological theory, characterized by an understanding that bodily parts (heart and lungs) and processes (oxygen in respiration) as part of a biological system, can be taught as a foundational concept to reason about physical activity. The effects of a biology-based intervention curriculum designed to teach preschool children about bodily functions as a part of the respiratory system, the role of oxygen as a vital substance and how physical activity acts an energy source were examined. Participants were recruited from three private preschool classrooms (two treatment; 1 control) in Southern California and included a total of 48 four-year-old children (30 treatment; 18 control). Findings from this study suggested that young children could be taught relevant biological concepts about the role of oxygen in respiratory processes. Children who received biology-based intervention curriculum made significant gains in their understanding of the biology of respiration, identification of physical and sedentary activities. In addition these children demonstrated that coherence of conceptual knowledge was correlated with improved accuracy at activity identification and reasoning about the inner workings of the body contributing to endurance. Findings from this study provided evidence to support the benefits of providing age appropriate but complex coherent biological instruction to children in early childhood settings.

EDITORIAL: Physical Biology

NASA Astrophysics Data System (ADS)

Roscoe, Jane

2004-06-01

Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at http://physbio.iop.org This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular tutorial `An introduction to cell motility for the physical scientist' by D A Fletcher and J A Theriot. Physical Biology offers a number of benefits to the author including free publication (no page or color charges), free multimedia enhancements, rapid publication and a large international readership. To ensure that Physical Biology is truly interdisciplinary and accessible to readers across a broad range of fields, the journal ultilizes a style editor. This unique service makes the journal indispensible to biologists and physicists alike. The feedback from both readers and authors on the use of style editing has been positive: `it is unusual in my experience for a journal to provide such guidance and it augurs well for Physical Biology's role in bridging the gap between the physical and biological sciences' S S Andrews, Lawrence Berkeley Laboratory, USA. You are invited to join the growing list of authors by submitting your work to this new, cutting-edge and rigorously peer-reviewed journal.

Networks In Real Space: Characteristics and Analysis for Biology and Mechanics

NASA Astrophysics Data System (ADS)

Modes, Carl; Magnasco, Marcelo; Katifori, Eleni

Functional networks embedded in physical space play a crucial role in countless biological and physical systems, from the efficient dissemination of oxygen, blood sugars, and hormonal signals in vascular systems to the complex relaying of informational signals in the brain to the distribution of stress and strain in architecture or static sand piles. Unlike their more-studied abstract cousins, such as the hyperlinked internet, social networks, or economic and financial connections, these networks are both constrained by and intimately connected to the physicality of their real, embedding space. We report on the results of new computational and analytic approaches tailored to these physical networks with particular implications and insights for mammalian organ vasculature.

Top-down models in biology: explanation and control of complex living systems above the molecular level.

PubMed

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Top-down models in biology: explanation and control of complex living systems above the molecular level

PubMed Central

2016-01-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. PMID:27807271

Information and material flows in complex networks

NASA Astrophysics Data System (ADS)

Helbing, Dirk; Armbruster, Dieter; Mikhailov, Alexander S.; Lefeber, Erjen

2006-04-01

In this special issue, an overview of the Thematic Institute (TI) on Information and Material Flows in Complex Systems is given. The TI was carried out within EXYSTENCE, the first EU Network of Excellence in the area of complex systems. Its motivation, research approach and subjects are presented here. Among the various methods used are many-particle and statistical physics, nonlinear dynamics, as well as complex systems, network and control theory. The contributions are relevant for complex systems as diverse as vehicle and data traffic in networks, logistics, production, and material flows in biological systems. The key disciplines involved are socio-, econo-, traffic- and bio-physics, and a new research area that could be called “biologistics”.

Environmental Modeling

EPA Pesticide Factsheets

EPA's modeling community is working to gain insights into certain parts of a physical, biological, economic, or social system by conducting environmental assessments for Agency decision making to complex environmental issues.

HYDROGEOLOGIC SETTING AND CHARACTERISTICS OF RIPARIAN MEADOW COMPLEXES IN THE MOUNTAINS OF CENTRAL NEVADA: A CASE STUDY

EPA Science Inventory

Riparian wet meadow complexes in the mountains of the central Great Basin are scarce, ecologically important systems threatened by stream incision. An interdisciplinary team from government and academia is investigating the origin, setting, and biological--physical interrelations...

Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

ERIC Educational Resources Information Center

Smith, John A.

2013-01-01

This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

Status and Prospects of Hirfl Experiments on Nuclear Physics

NASA Astrophysics Data System (ADS)

Xu, H. S.; Zheng, C.; Xiao, G. Q.; Zhan, W. L.; Zhou, X. H.; Zhang, Y. H.; Sun, Z. Y.; Wang, J. S.; Gan, Z. G.; Huang, W. X.; Ma, X. W.

HIRFL is an accelerator complex consisting of 3 accelerators, 2 radioactive beams lines, 1 storage rings and a number of experimental setups. The research activities at HIRFL cover the fields of radio-biology, material science, atomic physics, and nuclear physics. This report mainly concentrates on the experiments of nuclear physics with the existing and planned experimental setups such as SHANS, RIBLL1, ETF, CSRe, PISA and HPLUS at HIRFL.

Quantum physics meets biology

PubMed Central

Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

2009-01-01

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a “pedestrian guide” to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future “quantum biology,” its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena. PMID:20234806

Quantum physics meets biology.

PubMed

Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

2009-12-01

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a "pedestrian guide" to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future "quantum biology," its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.

Kinetics and Photochemistry of Ruthenium Bisbipyridine Diacetonitrile Complexes: An Interdisciplinary Inorganic and Physical Chemistry Laboratory Exercise

ERIC Educational Resources Information Center

Rapp, Teresa L.; Phillips, Susan R.; Dmochowski, Ivan J.

2016-01-01

The study of ruthenium polypyridyl complexes can be widely applied across disciplines in the undergraduate curriculum. Ruthenium photochemistry has advanced many fields including dye-sensitized solar cells, photoredox catalysis, lightdriven water oxidation, and biological electron transfer. Equally promising are ruthenium polypyridyl complexes…

Aerobic metabolism underlies complexity and capacity

PubMed Central

Koch, Lauren G; Britton, Steven L

2008-01-01

The evolution of biological complexity beyond single-celled organisms was linked temporally with the development of an oxygen atmosphere. Functionally, this linkage can be attributed to oxygen ranking high in both abundance and electronegativity amongst the stable elements of the universe. That is, reduction of oxygen provides for close to the largest possible transfer of energy for each electron transfer reaction. This suggests the general hypothesis that the steep thermodynamic gradient of an oxygen environment was permissive for the development of multicellular complexity. A corollary of this hypothesis is that aerobic metabolism underwrites complex biological function mechanistically at all levels of organization. The strong contemporary functional association of aerobic metabolism with both physical capacity and health is presumably a product of the integral role of oxygen in our evolutionary history. Here we provide arguments from thermodynamics, evolution, metabolic network analysis, clinical observations and animal models that are in accord with the centrality of oxygen in biology. PMID:17947307

Bayesian approach to MSD-based analysis of particle motion in live cells.

PubMed

Monnier, Nilah; Guo, Syuan-Ming; Mori, Masashi; He, Jun; Lénárt, Péter; Bathe, Mark

2012-08-08

Quantitative tracking of particle motion using live-cell imaging is a powerful approach to understanding the mechanism of transport of biological molecules, organelles, and cells. However, inferring complex stochastic motion models from single-particle trajectories in an objective manner is nontrivial due to noise from sampling limitations and biological heterogeneity. Here, we present a systematic Bayesian approach to multiple-hypothesis testing of a general set of competing motion models based on particle mean-square displacements that automatically classifies particle motion, properly accounting for sampling limitations and correlated noise while appropriately penalizing model complexity according to Occam's Razor to avoid over-fitting. We test the procedure rigorously using simulated trajectories for which the underlying physical process is known, demonstrating that it chooses the simplest physical model that explains the observed data. Further, we show that computed model probabilities provide a reliability test for the downstream biological interpretation of associated parameter values. We subsequently illustrate the broad utility of the approach by applying it to disparate biological systems including experimental particle trajectories from chromosomes, kinetochores, and membrane receptors undergoing a variety of complex motions. This automated and objective Bayesian framework easily scales to large numbers of particle trajectories, making it ideal for classifying the complex motion of large numbers of single molecules and cells from high-throughput screens, as well as single-cell-, tissue-, and organism-level studies. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Living matter—nexus of physics and biology in the 21st century

PubMed Central

Gardel, Margaret L.

2012-01-01

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes. PMID:23112229

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNamara, A; Held, K; Paganetti, H

2016-06-15

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecularmore » geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.« less

The Network Organization of Cancer-associated Protein Complexes in Human Tissues

PubMed Central

Zhao, Jing; Lee, Sang Hoon; Huss, Mikael; Holme, Petter

2013-01-01

Differential gene expression profiles for detecting disease genes have been studied intensively in systems biology. However, it is known that various biological functions achieved by proteins follow from the ability of the protein to form complexes by physically binding to each other. In other words, the functional units are often protein complexes rather than individual proteins. Thus, we seek to replace the perspective of disease-related genes by disease-related complexes, exemplifying with data on 39 human solid tissue cancers and their original normal tissues. To obtain the differential abundance levels of protein complexes, we apply an optimization algorithm to genome-wide differential expression data. From the differential abundance of complexes, we extract tissue- and cancer-selective complexes, and investigate their relevance to cancer. The method is supported by a clustering tendency of bipartite cancer-complex relationships, as well as a more concrete and realistic approach to disease-related proteomics. PMID:23567845

Biomedically relevant chemical and physical properties of coal combustion products.

PubMed Central

Fisher, G L

1983-01-01

The evaluation of the potential public and occupational health hazards of developing and existing combustion processes requires a detailed understanding of the physical and chemical properties of effluents available for human and environmental exposures. These processes produce complex mixtures of gases and aerosols which may interact synergistically or antagonistically with biological systems. Because of the physicochemical complexity of the effluents, the biomedically relevant properties of these materials must be carefully assessed. Subsequent to release from combustion sources, environmental interactions further complicate assessment of the toxicity of combustion products. This report provides an overview of the biomedically relevant physical and chemical properties of coal fly ash. Coal fly ash is presented as a model complex mixture for health and safety evaluation of combustion processes. PMID:6337824

Modeling and simulation of high dimensional stochastic multiscale PDE systems at the exascale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zabaras, Nicolas J.

2016-11-08

Predictive Modeling of multiscale and Multiphysics systems requires accurate data driven characterization of the input uncertainties, and understanding of how they propagate across scales and alter the final solution. This project develops a rigorous mathematical framework and scalable uncertainty quantification algorithms to efficiently construct realistic low dimensional input models, and surrogate low complexity systems for the analysis, design, and control of physical systems represented by multiscale stochastic PDEs. The work can be applied to many areas including physical and biological processes, from climate modeling to systems biology.

DURIP: Electrokinetic Injection and Separation System for Analysis of Protein and Peptide Transport, Adsorption and Kinetics Instrumentation Proposal

DTIC Science & Technology

2015-03-18

both the electric double layer that forms at a solid-liquid interface as well as the biomolecules themselves, we can harness the coupled physics of...the biomolecules themselves, we can harness the coupled physics of complex biological fluids in nanofluidic channels towards unique, efficient

Fire effects on belowground sustainability: A review and synthesis

Treesearch

Daniel G. Neary; Carole C. Klopatek; Leonard F. DeBano; Peter F. Ffolliott

1999-01-01

The overall effects of the fire on ecosystems are complex, ranging from the reduction or elimination of aboveground biomass to impacts on belowground physical, chemical and microbial mediated processes. Since a key component of overall ecosystem sustainability occurs belowground, recovery is tied to the soil's physical, chemical, and biological functions and...

Statistical Physics in the Era of Big Data

ERIC Educational Resources Information Center

Wang, Dashun

2013-01-01

With the wealth of data provided by a wide range of high-throughout measurement tools and technologies, statistical physics of complex systems is entering a new phase, impacting in a meaningful fashion a wide range of fields, from cell biology to computer science to economics. In this dissertation, by applying tools and techniques developed in…

Biological system interactions.

PubMed Central

Adomian, G; Adomian, G E; Bellman, R E

1984-01-01

Mathematical modeling of cellular population growth, interconnected subsystems of the body, blood flow, and numerous other complex biological systems problems involves nonlinearities and generally randomness as well. Such problems have been dealt with by mathematical methods often changing the actual model to make it tractable. The method presented in this paper (and referenced works) allows much more physically realistic solutions. PMID:6585837

A general mechanism for competitor-induced dissociation of molecular complexes

PubMed Central

Paramanathan, Thayaparan; Reeves, Daniel; Friedman, Larry J.; Kondev, Jane; Gelles, Jeff

2014-01-01

The kinetic stability of non-covalent macromolecular complexes controls many biological phenomena. Here we find that physical models of complex dissociation predict that competitor molecules will in general accelerate the breakdown of isolated bimolecular complexes by occluding rapid rebinding of the two binding partners. This prediction is largely independent of molecular details. We confirm the prediction with single-molecule fluorescence experiments on a well-characterized DNA strand dissociation reaction. Contrary to common assumptions, competitor–induced acceleration of dissociation can occur in biologically relevant competitor concentration ranges and does not necessarily implyternary association of competitor with the bimolecular complex. Thus, occlusion of complex rebinding may play a significant role in a variety of biomolecular processes. The results also show that single-molecule colocalization experiments can accurately measure dissociation rates despite their limited spatio temporal resolution. PMID:25342513

A generic framework for individual-based modelling and physical-biological interaction

PubMed Central

2018-01-01

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems. PMID:29351280

Challenges in Developing Models Describing Complex Soil Systems

NASA Astrophysics Data System (ADS)

Simunek, J.; Jacques, D.

2014-12-01

Quantitative mechanistic models that consider basic physical, mechanical, chemical, and biological processes have the potential to be powerful tools to integrate our understanding of complex soil systems, and the soil science community has often called for models that would include a large number of these diverse processes. However, once attempts have been made to develop such models, the response from the community has not always been overwhelming, especially after it discovered that these models are consequently highly complex, requiring not only a large number of parameters, not all of which can be easily (or at all) measured and/or identified, and which are often associated with large uncertainties, but also requiring from their users deep knowledge of all/most of these implemented physical, mechanical, chemical and biological processes. Real, or perceived, complexity of these models then discourages users from using them even for relatively simple applications, for which they would be perfectly adequate. Due to the nonlinear nature and chemical/biological complexity of the soil systems, it is also virtually impossible to verify these types of models analytically, raising doubts about their applicability. Code inter-comparisons, which is then likely the most suitable method to assess code capabilities and model performance, requires existence of multiple models of similar/overlapping capabilities, which may not always exist. It is thus a challenge not only to developed models describing complex soil systems, but also to persuade the soil science community in using them. As a result, complex quantitative mechanistic models are still an underutilized tool in soil science research. We will demonstrate some of the challenges discussed above on our own efforts in developing quantitative mechanistic models (such as HP1/2) for complex soil systems.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

PubMed Central

Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

2011-01-01

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

An engineering paradigm in the biomedical sciences: Knowledge as epistemic tool.

PubMed

Boon, Mieke

2017-10-01

In order to deal with the complexity of biological systems and attempts to generate applicable results, current biomedical sciences are adopting concepts and methods from the engineering sciences. Philosophers of science have interpreted this as the emergence of an engineering paradigm, in particular in systems biology and synthetic biology. This article aims at the articulation of the supposed engineering paradigm by contrast with the physics paradigm that supported the rise of biochemistry and molecular biology. This articulation starts from Kuhn's notion of a disciplinary matrix, which indicates what constitutes a paradigm. It is argued that the core of the physics paradigm is its metaphysical and ontological presuppositions, whereas the core of the engineering paradigm is the epistemic aim of producing useful knowledge for solving problems external to the scientific practice. Therefore, the two paradigms involve distinct notions of knowledge. Whereas the physics paradigm entails a representational notion of knowledge, the engineering paradigm involves the notion of 'knowledge as epistemic tool'. Copyright © 2017 Elsevier Ltd. All rights reserved.

Maximizing the Adjacent Possible in Automata Chemistries.

PubMed

Hickinbotham, Simon; Clark, Edward; Nellis, Adam; Stepney, Susan; Clarke, Tim; Young, Peter

2016-01-01

Automata chemistries are good vehicles for experimentation in open-ended evolution, but they are by necessity complex systems whose low-level properties require careful design. To aid the process of designing automata chemistries, we develop an abstract model that classifies the features of a chemistry from a physical (bottom up) perspective and from a biological (top down) perspective. There are two levels: things that can evolve, and things that cannot. We equate the evolving level with biology and the non-evolving level with physics. We design our initial organisms in the biology, so they can evolve. We design the physics to facilitate evolvable biologies. This architecture leads to a set of design principles that should be observed when creating an instantiation of the architecture. These principles are Everything Evolves, Everything's Soft, and Everything Dies. To evaluate these ideas, we present experiments in the recently developed Stringmol automata chemistry. We examine the properties of Stringmol with respect to the principles, and so demonstrate the usefulness of the principles in designing automata chemistries.

Remotely controlled fusion of selected vesicles and living cells: a key issue review

NASA Astrophysics Data System (ADS)

Bahadori, Azra; Moreno-Pescador, Guillermo; Oddershede, Lene B.; Bendix, Poul M.

2018-03-01

Remote control over fusion of single cells and vesicles has a great potential in biological and chemical research allowing both transfer of genetic material between cells and transfer of molecular content between vesicles. Membrane fusion is a critical process in biology that facilitates molecular transport and mixing of cellular cytoplasms with potential formation of hybrid cells. Cells precisely regulate internal membrane fusions with the aid of specialized fusion complexes that physically provide the energy necessary for mediating fusion. Physical factors like membrane curvature, tension and temperature, affect biological membrane fusion by lowering the associated energy barrier. This has inspired the development of physical approaches to harness the fusion process at a single cell level by using remotely controlled electromagnetic fields to trigger membrane fusion. Here, we critically review various approaches, based on lasers or electric pulses, to control fusion between individual cells or between individual lipid vesicles and discuss their potential and limitations for present and future applications within biochemistry, biology and soft matter.

Introductory Physics Laboratories for Life Scientists - Hands on Physics of Complex Systems

NASA Astrophysics Data System (ADS)

Losert, Wolfgang; Moore, Kim

2015-03-01

We have developed a set of laboratories and hands on activities to accompany a new two-semester interdisciplinary physics course that has been successfully implemented as the required physics course for premeds at the University of Maryland. The laboratories include significant content on physics relevant to cellular scales, from chemical interactions to random motion and charge screening in fluids. We also introduce the students to research-grade equipment and modern physics analysis tools in contexts relevant to biology, while maintaining the pedagogically valuable open-ended laboratory structure of reformed laboratories.

Health: The No-Man's-Land Between Physics and Biology.

PubMed

Mansfield, Peter J

2015-10-01

Health as a positive attribute is poorly understood because understanding requires concepts from physics, of which physicians and other life scientists have a very poor grasp. This paper reviews the physics that bears on biology, in particular complex quaternions and scalar fields, relates these to the morphogenetic fields proposed by biologists, and defines health as an attribute of living action within these fields. The distinction of quality, as juxtaposed with quantity, proves essential. Its basic properties are set out, but a science and mathematics of quality are awaited. The implications of this model are discussed, particularly as proper health enhancement could set a natural limit to demand for, and therefore the cost of, medical services.

Recent advances in mathematical criminology. Comment on "Statistical physics of crime: A review" by M.R. D'Orsogna and M. Perc

NASA Astrophysics Data System (ADS)

Rodríguez, Nancy

2015-03-01

The use of mathematical tools has long proved to be useful in gaining understanding of complex systems in physics [1]. Recently, many researchers have realized that there is an analogy between emerging phenomena in complex social systems and complex physical or biological systems [4,5,12]. This realization has particularly benefited the modeling and understanding of crime, a ubiquitous phenomena that is far from being understood. In fact, when one is interested in the bulk behavior of patterns that emerge from small and seemingly unrelated interactions as well as decisions that occur at the individual level, the mathematical tools that have been developed in statistical physics, game theory, network theory, dynamical systems, and partial differential equations can be useful in shedding light into the dynamics of these patterns [2-4,6,12].

Future Directions in Medical Physics

NASA Astrophysics Data System (ADS)

Jeraj, Robert

Medical Physics is a highly interdisciplinary field at the intersection between physics and medicine and biology. Medical Physics is aiming at development of novel applications of physical processes and techniques in various areas of medicine and biology. Medical Physics had and continues to have profound impact by developing improved imaging and treatment technologies, and helping to advance our understanding of the complexity of the disease. The general trend in medicine towards personalized therapy, and emphasis on accelerated translational research is having a profound impact on medical physics as well. In the traditional stronghold for medical physicists - radiation therapy - the new reality is shaping in the form of biologically conformal and combination therapies, as well as advanced particle therapy approaches, such as proton and ion therapies. Rapid increase in faster and more informative multi-modality medical imaging is bringing a wealth of information that is being complemented with data obtained from genomic profiling and other biomarkers. Novel data analysis and data mining approaches are proving grounds for employment of various artificial intelligence methods that will help further improving clinical decision making for optimization of various therapies as well as better understanding of the disease properties and disease evolution, ultimately leading to improved clinical outcomes.

Teaching Energy Concepts by Working on Themes of Cultural and Environmental Value

ERIC Educational Resources Information Center

Besson, Ugo; De Ambrosis, Anna

2014-01-01

Energy is a central topic in physics and a key concept for understanding the physical, biological and technological worlds. It is a complex topic with multiple connections with different areas of science and with social, environmental and philosophical issues. In this paper we discuss some aspects of the teaching and learning of the energy…

Measurement Frontiers in Molecular Biology

NASA Astrophysics Data System (ADS)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

Toward self-organization and complex matter.

PubMed

Lehn, Jean-Marie

2002-03-29

Beyond molecular chemistry based on the covalent bond, supramolecular chemistry aims at developing highly complex chemical systems from components interacting through noncovalent intermolecular forces. Over the past quarter century, supramolecular chemistry has grown into a major field and has fueled numerous developments at the interfaces with biology and physics. Some of the conceptual advances and future challenges are profiled here.

UNCERTAINTY ON RADIATION DOSES ESTIMATED BY BIOLOGICAL AND RETROSPECTIVE PHYSICAL METHODS.

PubMed

Ainsbury, Elizabeth A; Samaga, Daniel; Della Monaca, Sara; Marrale, Maurizio; Bassinet, Celine; Burbidge, Christopher I; Correcher, Virgilio; Discher, Michael; Eakins, Jon; Fattibene, Paola; Güçlü, Inci; Higueras, Manuel; Lund, Eva; Maltar-Strmecki, Nadica; McKeever, Stephen; Rääf, Christopher L; Sholom, Sergey; Veronese, Ivan; Wieser, Albrecht; Woda, Clemens; Trompier, Francois

2018-03-01

Biological and physical retrospective dosimetry are recognised as key techniques to provide individual estimates of dose following unplanned exposures to ionising radiation. Whilst there has been a relatively large amount of recent development in the biological and physical procedures, development of statistical analysis techniques has failed to keep pace. The aim of this paper is to review the current state of the art in uncertainty analysis techniques across the 'EURADOS Working Group 10-Retrospective dosimetry' members, to give concrete examples of implementation of the techniques recommended in the international standards, and to further promote the use of Monte Carlo techniques to support characterisation of uncertainties. It is concluded that sufficient techniques are available and in use by most laboratories for acute, whole body exposures to highly penetrating radiation, but further work will be required to ensure that statistical analysis is always wholly sufficient for the more complex exposure scenarios.

Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations

PubMed Central

Liao, David; Tlsty, Thea D.

2014-01-01

The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely ‘empirical’ equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments. PMID:25097752

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed Central

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system’s behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics. PMID:29163041

The Biophysics Microgravity Initiative

NASA Technical Reports Server (NTRS)

Gorti, S.

2016-01-01

Biophysical microgravity research on the International Space Station using biological materials has been ongoing for several decades. The well-documented substantive effects of long duration microgravity include the facilitation of the assembly of biological macromolecules into large structures, e.g., formation of large protein crystals under micro-gravity. NASA is invested not only in understanding the possible physical mechanisms of crystal growth, but also promoting two flight investigations to determine the influence of µ-gravity on protein crystal quality. In addition to crystal growth, flight investigations to determine the effects of shear on nucleation and subsequent formation of complex structures (e.g., crystals, fibrils, etc.) are also supported. It is now considered that long duration microgravity research aboard the ISS could also make possible the formation of large complex biological and biomimetic materials. Investigations of various materials undergoing complex structure formation in microgravity will not only strengthen NASA science programs, but may also provide invaluable insight towards the construction of large complex tissues, organs, or biomimetic materials on Earth.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system's behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics.

Synchronization in complex networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arenas, A.; Diaz-Guilera, A.; Moreno, Y.

Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization phenomena in natural systems take now advantage of the recent theory of complex networks. In this review, we report the advances in the comprehension of synchronization phenomena when oscillating elements are constrained to interact in a complex network topology. We also overview the new emergent features coming out from the interplay between the structure and the function of the underlying pattern of connections. Extensive numerical work as well as analyticalmore » approaches to the problem are presented. Finally, we review several applications of synchronization in complex networks to different disciplines: biological systems and neuroscience, engineering and computer science, and economy and social sciences.« less

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents biology, chemistry, physics, and health activities, experiments, demonstrations, and computer programs. Includes mechanism of stomatal opening, using aquatic plants to help demonstrate chemical buffering, microbial activity/contamination in milk samples, computer computation of fitness scores, reservoir project, complexes of transition…

How do biological systems discriminate among physically similar ions?

PubMed

Diamond, J M

1975-10-01

This paper reviews the history of understanding how biological systems can discriminate so strikingly among physically similar ions, especially alkali cations. Appreciation of qualitative regularities ("permitted sequences") and quantitative regularities ("selectivity isotherms") in ion selectivity grew first from studies of ion exchangers and glass electrodes, then of biological systems such as enzymes and cell membranes, and most recently of lipid bilayers doped with model pores and carriers. Discrimination of ions depends on both electrostatic and steric forces. "Black-box" studies on intact biological membranes have in some cases yielded molecular clues to the structure of the actual biological pores and carriers. Major current problems involve the extraction of these molecules; how to do it, what to do when it is achieved, and how (and if) it is relevant to the central problems of membrane function. Further advances are expected soon from studies of rate barriers within membranes, of voltage-dependent ("excitable") conducting channels, and of increasingly complex model systems and biological membranes.

PREFACE: Nanobiology: from physics and engineering to biology

NASA Astrophysics Data System (ADS)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of shapes and materials. Inspection of the protein structure databank illustrates the breadth of scaffolds, shapes and properties that protein molecules and their building blocks can provide. Via a shape-guided self-assembly strategy, these can be put together toward a specific function. Further, by inserting synthetic non-natural residues at judiciously selected positions, or synthetic peptide linkers, we may selectively rigidify the construct, or obtain a totally new world of shapes and scaffolds. Such broadening of the chemical space may lead to an almost unlimited range of nanosystems and architectures. Merging computation with experiment will accelerate nanodesign. Computational modeling will enhance the application of nanotechnology to key areas such as drug delivery and biomaterial design. Nanobiology is a field where interdisciplinary collaborations are essential and disciplines converge. Discipline convergence should enable the quantitation, leading to a better understanding of the regulatory networks within cells and between cells of an organism. These networks dictate how a cell responds to external stimuli, which in turn activate signaling cascades. It should allow the addressing of a broad range of questions on the structure and function of the cytoskeleton; the nuclear envelope; signal transduction by membrane embedded receptors; the nanomechanical properties of the extracellular matrix; nuclear transport; and voltage induced channel gating. For successful nanostructure design, we need to figure out and be able to control the intermolecular associations. For a stable functional construct, there are two key elements: first, the conformations of the building blocks in the designed structure should follow their natural tendencies; and second, the associations should be favorable. Molecules interact through their surfaces. Thus, favorable associations derive from shape complementarity and contributions of the various physical components. Nanobiology is in its infancy. Yet, biology provides an enormous range of engaging and stimulating problems with many in vivo examples of intricate, complex, fascinating biological systems. Understanding, mimicking and controlling the devices which target these processes and which are constructed from these molecules is a tremendous challenge to the converging disciplines in nanobiology.

Using simple manipulatives to improve student comprehension of a complex biological process: protein synthesis.

PubMed

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article describes an exercise that was developed to illustrate the process of translation using simple objects to represent complex molecules. Animations, 3D physical models, computer simulations, laboratory experiments and classroom lectures are also used to reinforce the students' understanding of translation, but by focusing on the simple manipulatives in this exercise, students are better able to visualize concepts that can elude them when using the other methods. The translation exercise is described along with suggestions for background material, questions used to evaluate student comprehension and tips for using the manipulatives to identify common misconceptions. Copyright © 2012 Wiley Periodicals, Inc.

Supraglacial sulfur springs and associated biological activity in the Canadian high arctic - signs of life beneath the ice

USGS Publications Warehouse

Grasby, Stephen E.; Allen, Carlton C.; Longazo, Teresa G.; Lisle, John T.; Griffin, Dale W.; Beauchamp, Benoit

2003-01-01

Unique springs, discharging from the surface of an arctic glacier, release H2S and deposit native sulfur, gypsum, and calcite. The presence of sulfur in three oxidation states indicates a complex series of redox reactions. Physical and chemical conditions of the spring water and surrounding environment, as well as mineralogical and isotopic signatures, suggest biologically mediated reactions. Cell counts and DNA analyses confirm bacteria are present in the spring system, and a limited number of sequenced isolates suggests that complex communities of bacteria live within the glacial system.

Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

USGS Publications Warehouse

Rieman, Bruce; Dunham, Jason B.; Clayton, James

2006-01-01

Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions. Two solutions have been proposed to guide management in the face of that uncertainty: the use of “natural variability” in key environmental patterns, processes, or disturbance as a reference; and the retention of some areas as essentially unmanaged reserves to conserve and represent as much biological diversity as possible. Both concepts are scale dependent because dominant processes or patterns that might be referenced will change with scale. Context and linkages across scales may be as important in structuring biological systems as conditions within habitats used by individual organisms. Both ideas view the physical environment as a template for expression, maintenance, and evolution of ecological diversity. To conserve or restore a diverse physical template it will be important to recognize the ecologically important differences in physical characteristics and processes among streams or watersheds that we might attempt to mimic in management or represent in conservation or restoration reserves.

Pragmatic information in biology and physics.

PubMed

Roederer, Juan G

2016-03-13

I will show how an objective definition of the concept of information and the consideration of recent results about information processing in the human brain help clarify some fundamental aspects of physics and biology. Rather than attempting to define information ab initio, I introduce the concept of interaction between material bodies as a primary concept. Two distinct categories can be identified: (i) interactions which can always be reduced to a superposition of physical interactions (forces) between elementary constituents; and (ii) interactions between complex bodies which cannot be expressed as a superposition of interactions between parts, and in which patterns and forms (in space and/or time) play the determining role. Pragmatic information is then defined as the link between a given pattern and the ensuing pattern-specific change. I will show that pragmatic information is a biological concept; it plays no active role in the purely physical domain-it only does so when a living organism intervenes. The consequences for physics (including foundations of quantum mechanics) and biology (including brain function) will be discussed. This will include speculations about three fundamental transitions, from the quantum to the classical domain, from natural inanimate to living systems, and from subhuman to human brain information-processing operations, introduced here in their direct connection with the concept of pragmatic information. © 2016 The Author(s).

Fitting in or Opting Out: A Review of Key Social-Psychological Factors Influencing a Sense of Belonging for Women in Physics

ERIC Educational Resources Information Center

Lewis, Karyn L.; Stout, Jane G.; Pollack, Steven J.; Finkelstein, Noah D.; Ito, Tiffany A.

2016-01-01

A number of cultural, social, environmental, and biological factors have been suggested to explain women's relatively lower representation in physics and other science, technology, engineering, and math (STEM) fields. Given its persistence, the causes of gender disparities are likely to be complex and multiply determined. In this review paper, we…

The Hippo-YAP signaling pathway and contact inhibition of growth

PubMed Central

Gumbiner, Barry M.; Kim, Nam-Gyun

2014-01-01

ABSTRACT The Hippo-YAP pathway mediates the control of cell proliferation by contact inhibition as well as other attributes of the physical state of cells in tissues. Several mechanisms sense the spatial and physical organization of cells, and function through distinct upstream modules to stimulate Hippo-YAP signaling: adherens junction or cadherin–catenin complexes, epithelial polarity and tight junction complexes, the FAT-Dachsous morphogen pathway, as well as cell shape, actomyosin or mechanotransduction. Soluble extracellular factors also regulate Hippo pathway signaling, often inhibiting its activity. Indeed, the Hippo pathway mediates a reciprocal relationship between contact inhibition and mitogenic signaling. As a result, cells at the edges of a colony, a wound in a tissue or a tumor are more sensitive to ambient levels of growth factors and more likely to proliferate, migrate or differentiate through a YAP and/or TAZ-dependent process. Thus, the Hippo-YAP pathway senses and responds to the physical organization of cells in tissues and coordinates these physical cues with classic growth-factor-mediated signaling pathways. This Commentary is focused on the biological significance of Hippo-YAP signaling and how upstream regulatory modules of the pathway interact to produce biological outcomes. PMID:24532814

Live-cell imaging of invasion and intravasation in an artificial microvessel platform.

PubMed

Wong, Andrew D; Searson, Peter C

2014-09-01

Methods to visualize metastasis exist, but additional tools to better define the biologic and physical processes underlying invasion and intravasation are still needed. One difficulty in studying metastasis stems from the complexity of the interface between the tumor microenvironment and the vascular system. Here, we report the development of an investigational platform that positions tumor cells next to an artificial vessel embedded in an extracellular matrix. On this platform, we used live-cell fluorescence microscopy to analyze the complex interplay between metastatic cancer cells and a functional artificial microvessel that was lined with endothelial cells. The platform recapitulated known interactions, and its use demonstrated the capabilities for a systematic study of novel physical and biologic parameters involved in invasion and intravasation. In summary, our work offers an important new tool to advance knowledge about metastasis and candidate antimetastatic therapies. ©2014 American Association for Cancer Research.

Biological roles of glycans

PubMed Central

Varki, Ajit

2017-01-01

Abstract Simple and complex carbohydrates (glycans) have long been known to play major metabolic, structural and physical roles in biological systems. Targeted microbial binding to host glycans has also been studied for decades. But such biological roles can only explain some of the remarkable complexity and organismal diversity of glycans in nature. Reviewing the subject about two decades ago, one could find very few clear-cut instances of glycan-recognition-specific biological roles of glycans that were of intrinsic value to the organism expressing them. In striking contrast there is now a profusion of examples, such that this updated review cannot be comprehensive. Instead, a historical overview is presented, broad principles outlined and a few examples cited, representing diverse types of roles, mediated by various glycan classes, in different evolutionary lineages. What remains unchanged is the fact that while all theories regarding biological roles of glycans are supported by compelling evidence, exceptions to each can be found. In retrospect, this is not surprising. Complex and diverse glycans appear to be ubiquitous to all cells in nature, and essential to all life forms. Thus, >3 billion years of evolution consistently generated organisms that use these molecules for many key biological roles, even while sometimes coopting them for minor functions. In this respect, glycans are no different from other major macromolecular building blocks of life (nucleic acids, proteins and lipids), simply more rapidly evolving and complex. It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences. PMID:27558841

Complex network problems in physics, computer science and biology

NASA Astrophysics Data System (ADS)

Cojocaru, Radu Ionut

There is a close relation between physics and mathematics and the exchange of ideas between these two sciences are well established. However until few years ago there was no such a close relation between physics and computer science. Even more, only recently biologists started to use methods and tools from statistical physics in order to study the behavior of complex system. In this thesis we concentrate on applying and analyzing several methods borrowed from computer science to biology and also we use methods from statistical physics in solving hard problems from computer science. In recent years physicists have been interested in studying the behavior of complex networks. Physics is an experimental science in which theoretical predictions are compared to experiments. In this definition, the term prediction plays a very important role: although the system is complex, it is still possible to get predictions for its behavior, but these predictions are of a probabilistic nature. Spin glasses, lattice gases or the Potts model are a few examples of complex systems in physics. Spin glasses and many frustrated antiferromagnets map exactly to computer science problems in the NP-hard class defined in Chapter 1. In Chapter 1 we discuss a common result from artificial intelligence (AI) which shows that there are some problems which are NP-complete, with the implication that these problems are difficult to solve. We introduce a few well known hard problems from computer science (Satisfiability, Coloring, Vertex Cover together with Maximum Independent Set and Number Partitioning) and then discuss their mapping to problems from physics. In Chapter 2 we provide a short review of combinatorial optimization algorithms and their applications to ground state problems in disordered systems. We discuss the cavity method initially developed for studying the Sherrington-Kirkpatrick model of spin glasses. We extend this model to the study of a specific case of spin glass on the Bethe lattice at zero temperature and then we apply this formalism to the K-SAT problem defined in Chapter 1. The phase transition which physicists study often corresponds to a change in the computational complexity of the corresponding computer science problem. Chapter 3 presents phase transitions which are specific to the problems discussed in Chapter 1 and also known results for the K-SAT problem. We discuss the replica method and experimental evidences of replica symmetry breaking. The physics approach to hard problems is based on replica methods which are difficult to understand. In Chapter 4 we develop novel methods for studying hard problems using methods similar to the message passing techniques that were discussed in Chapter 2. Although we concentrated on the symmetric case, cavity methods show promise for generalizing our methods to the un-symmetric case. As has been highlighted by John Hopfield, several key features of biological systems are not shared by physical systems. Although living entities follow the laws of physics and chemistry, the fact that organisms adapt and reproduce introduces an essential ingredient that is missing in the physical sciences. In order to extract information from networks many algorithm have been developed. In Chapter 5 we apply polynomial algorithms like minimum spanning tree in order to study and construct gene regulatory networks from experimental data. As future work we propose the use of algorithms like min-cut/max-flow and Dijkstra for understanding key properties of these networks.

Cross-scale morphology

USGS Publications Warehouse

Allen, Craig R.; Holling, Crawford S.; Garmestani, Ahjond S.; El-Shaarawi, Abdel H.; Piegorsch, Walter W.

2013-01-01

The scaling of physical, biological, ecological and social phenomena is a major focus of efforts to develop simple representations of complex systems. Much of the attention has been on discovering universal scaling laws that emerge from simple physical and geometric processes. However, there are regular patterns of departures both from those scaling laws and from continuous distributions of attributes of systems. Those departures often demonstrate the development of self-organized interactions between living systems and physical processes over narrower ranges of scale.

HANDBOOK: GROUNDWATER - METHODOLOGY - VOL. 2

EPA Science Inventory

The subsurface environment of ground water is characterized by a complex interplay of physical, geochemical and biological forces that govern the release, transport and fate of a variety of chemical substances. There are literally as many varied hydrogeologic settings as there ar...

CHARACTERIZING CORAL CONDITION USING ESTIMATES OF THREE-DIMENSIONAL COLONY SURFACE AREA

EPA Science Inventory

Coral reefs provide shoreline protection, biological diversity, fishery harvets, and tourism, all values that stem from the physically-complex coral infrastructure. Stony corals (scleractinianss) construct and maintain the reef through deposition of calcium carbonate. Therefore...

Chimaera simulation of complex states of flowing matter.

PubMed

Succi, S

2016-11-13

We discuss a unified mesoscale framework (chimaera) for the simulation of complex states of flowing matter across scales of motion. The chimaera framework can deal with each of the three macro-meso-micro levels through suitable 'mutations' of the basic mesoscale formulation. The idea is illustrated through selected simulations of complex micro- and nanoscale flows.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

The Physics of Open Ended Evolution

NASA Astrophysics Data System (ADS)

Adams, Alyssa M.

What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory ought to be broad enough as to not be constrained to an Earth-based biochemistry. In this dissertation, the philosophy of studying living systems from the perspective of traditional physics is first explored as a motivating discussion for subsequent research. Traditionally, we have often thought of the physical world from a bottom-up approach: things happening on a smaller scale aggregate into things happening on a larger scale. In addition, the laws of physics are generally considered static over time. Research suggests that biological evolution may follow dynamic laws that (at least in part) change as a function of the state of the system. Of the three featured research projects, cellular automata (CA) are used as a model to study certain aspects of living systems in two of them. These aspects include self-reference, open-ended evolution, local physical universality, subjectivity, and information processing. Open-ended evolution and local physical universality are attributed to the vast amount of innovation observed throughout biological evolution. Biological systems may distinguish themselves in terms of information processing and storage, not outside the theory of computation. The final research project concretely explores real-world phenomenon by means of mapping dominance hierarchies in the evolution of video game strategies. Though the main question of how life differs from non-life remains unanswered, the mechanisms behind open-ended evolution and physical universality are revealed.

Hands-on-Entropy, Energy Balance with Biological Relevance

NASA Astrophysics Data System (ADS)

Reeves, Mark

2015-03-01

Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is important contribution of the entropy in driving fundamental biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy). This has enabled students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce complex biological processes and structures in order model them mathematically to account for both deterministic and probabilistic processes. The students test these models in simulations and in laboratory experiments that are biologically relevant such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront random forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory physics with a bio focus. Supported by NSF DUE.

Molecular Mechanics and Dynamics Characterization of an "in silico" Mutated Protein: A Stand-Alone Lab Module or Support Activity for "in vivo" and "in vitro" Analyses of Targeted Proteins

ERIC Educational Resources Information Center

Chiang, Harry; Robinson, Lucy C.; Brame, Cynthia J.; Messina, Troy C.

2013-01-01

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems.…

The Emergence of Temporal Structures in Dynamical Systems

NASA Astrophysics Data System (ADS)

Mainzer, Klaus

2010-10-01

Dynamical systems in classical, relativistic and quantum physics are ruled by laws with time reversibility. Complex dynamical systems with time-irreversibility are known from thermodynamics, biological evolution, growth of organisms, brain research, aging of people, and historical processes in social sciences. Complex systems are systems that compromise many interacting parts with the ability to generate a new quality of macroscopic collective behavior the manifestations of which are the spontaneous emergence of distinctive temporal, spatial or functional structures. But, emergence is no mystery. In a general meaning, the emergence of macroscopic features results from the nonlinear interactions of the elements in a complex system. Mathematically, the emergence of irreversible structures is modelled by phase transitions in non-equilibrium dynamics of complex systems. These methods have been modified even for chemical, biological, economic and societal applications (e.g., econophysics). Emergence of irreversible structures can also be simulated by computational systems. The question arises how the emergence of irreversible structures is compatible with the reversibility of fundamental physical laws. It is argued that, according to quantum cosmology, cosmic evolution leads from symmetry to complexity of irreversible structures by symmetry breaking and phase transitions. Thus, arrows of time and aging processes are not only subjective experiences or even contradictions to natural laws, but they can be explained by quantum cosmology and the nonlinear dynamics of complex systems. Human experiences and religious concepts of arrows of time are considered in a modern scientific framework. Platonic ideas of eternity are at least understandable with respect to mathematical invariance and symmetry of physical laws. Heraclit’s world of change and dynamics can be mapped onto our daily real-life experiences of arrows of time.

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

NASA Astrophysics Data System (ADS)

Benza, Vincenzo G.; Bassetti, Bruno; Dorfman, Kevin D.; Scolari, Vittore F.; Bromek, Krystyna; Cicuta, Pietro; Cosentino Lagomarsino, Marco

2012-07-01

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.

Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks

PubMed Central

2018-01-01

Signaling pathways represent parts of the global biological molecular network which connects them into a seamless whole through complex direct and indirect (hidden) crosstalk whose structure can change during development or in pathological conditions. We suggest a novel methodology, called Googlomics, for the structural analysis of directed biological networks using spectral analysis of their Google matrices, using parallels with quantum scattering theory, developed for nuclear and mesoscopic physics and quantum chaos. We introduce analytical “reduced Google matrix” method for the analysis of biological network structure. The method allows inferring hidden causal relations between the members of a signaling pathway or a functionally related group of genes. We investigate how the structure of hidden causal relations can be reprogrammed as a result of changes in the transcriptional network layer during cancerogenesis. The suggested Googlomics approach rigorously characterizes complex systemic changes in the wiring of large causal biological networks in a computationally efficient way. PMID:29370181

A short note on the paper of Liu et al. (2012). A relative Lempel-Ziv complexity: Application to comparing biological sequences. Chemical Physics Letters, volume 530, 19 March 2012, pages 107-112

NASA Astrophysics Data System (ADS)

Arit, Turkan; Keskin, Burak; Firuzan, Esin; Cavas, Cagin Kandemir; Liu, Liwei; Cavas, Levent

2018-04-01

The report entitled "L. Liu, D. Li, F. Bai, A relative Lempel-Ziv complexity: Application to comparing biological sequences, Chem. Phys. Lett. 530 (2012) 107-112" mentions on the powerful construction of phylogenetic trees based on Lempel-Ziv algorithm. On the other hand, the method explained in the paper does not give promising result on the data set on invasive Caulerpa taxifolia in the Mediterranean Sea. The phylogenetic trees are obtained by the proposed method of the aforementioned paper in this short note.

Shannon information, LMC complexity and Rényi entropies: a straightforward approach.

PubMed

López-Ruiz, Ricardo

2005-04-01

The LMC complexity, an indicator of complexity based on a probabilistic description, is revisited. A straightforward approach allows us to establish the time evolution of this indicator in a near-equilibrium situation and gives us a new insight for interpreting the LMC complexity for a general non equilibrium system. Its relationship with the Rényi entropies is also explained. One of the advantages of this indicator is that its calculation does not require a considerable computational effort in many cases of physical and biological interest.

Pharmacological Role of Anions (Sulphate, Nitrate, Oxalate and Acetate) on the Antibacterial Activity of Cobalt(II), Copper(II) and Nickel(II) Complexes With Nicotinoylhydrazine-Derived ONO, NNO and SNO Ligands

PubMed Central

Rauf, Abdur

1996-01-01

Mixed ligands biologically active complexes of cobalt(II), copper(II) and nickel(II) with nicotinoylhydrazine-derived ONO, NNO and SNO donor schiff-base ligands having the same metal ion but different anions such as sulphate, nitrate, oxalate and acetate have been synthesised and characterised on the basis of their physical, analytical and spectral data. In order to evaluate the role of anions on their bioability, these ligands and their synthesised metal complexes with various anions have been screened against bacterial species such as Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus and the title studies have proved a definative role of anions in increasing the biological activity PMID:18472896

Synthesis, characterization and biological properties of thienyl derived triazole Schiff bases and their oxovanadium(IV) complexes.

PubMed

Chohan, Zahid H; Sumrra, Sajjad H

2012-04-01

A new series of biologically active thienyl derived triazole Schiff bases and their oxovanadium(IV) complexes have been synthesized and characterized on the basis of physical (m.p., magnetic susceptibility and conductivity), spectral (IR, ¹H and ¹³C NMR, electronic and mass spectrometry) and microanalytical data. All the Schiff base ligands and their oxovanadium(IV) complexes have been subjected to in vitro antibacterial activity against four Gram-negative (Escherichia coli, Shigella flexneri, Pseudomonas aeruginosa, Salmonella enterica serover typhi) and two Gram-positive (Staphylococcus aureus and Bacillus subtilis) bacterial strains and, for in vitro antifungal activity against Trichophyton longifucus, Candida albican, Aspergillus flavus, Microscopum canis, Fusarium solani and Candida glabrata. Brine shrimp bioassay was also carried out to check the cytotoxic nature of these compounds.

Some biologically active oxovanadium(IV) complexes of triazole derived Schiff bases: their synthesis, characterization and biological properties.

PubMed

Chohan, Zahid H; Sumrra, Sajjad H

2010-10-01

A series of biologically active oxovanadium(IV) complexes of triazole derived Schiff bases L(1)-L(5) have been synthesized and characterized by their physical, analytical, and spectral data. The synthesized ligands potentially act as bidentate, in which the oxygen of furfural and nitrogen of azomethine coordinate with the oxovanadium atom to give a stoichiometry of vanadyl complexes 1:2 (M:L) in a square-pyramidal geometry. In vitro antibacterial and antifungal activities on different species of pathogenic bacteria (E. coli, S. flexneri, P. aeruginosa, S. typhi, S. aureus, and B. subtilis) and fungi (T. longifusus, C. albicans, A. flavus, M. canis, F. solani, and C. glabrata) have been studied. All compounds showed moderate to significant antibacterial activity against one or more bacterial strains and good antifungal activity against most of the fungal strains. The brine shrimp bioassay was also carried out to check the cytotoxicity of coordinated and uncoordinated synthesized compounds.

Drawdown Effects on Lake and Reservoir Physical Habitat - a National Picture

EPA Science Inventory

Structural complexity at the land-water interface of lakes promotes interchange of water, nutrients and energy; and provides diverse habitat for aquatic and terrestrial organisms. Shoreline zones are hot-spots for both biological diversity and human activity. Lake level fluctuat...

An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

PubMed Central

Febrer, Melanie; Goicoechea, Jose Luis; Wright, Jonathan; McKenzie, Neil; Song, Xiang; Lin, Jinke; Collura, Kristi; Wissotski, Marina; Yu, Yeisoo; Ammiraju, Jetty S. S.; Wolny, Elzbieta; Idziak, Dominika; Betekhtin, Alexander; Kudrna, Dave; Hasterok, Robert; Wing, Rod A.; Bevan, Michael W.

2010-01-01

The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation. PMID:20976139

Interdisciplinary education - a predator-prey model for developing a skill set in mathematics, biology and technology

NASA Astrophysics Data System (ADS)

van der Hoff, Quay

2017-08-01

The science of biology has been transforming dramatically and so the need for a stronger mathematical background for biology students has increased. Biological students reaching the senior or post-graduate level often come to realize that their mathematical background is insufficient. Similarly, students in a mathematics programme, interested in biological phenomena, find it difficult to master the complex systems encountered in biology. In short, the biologists do not have enough mathematics and the mathematicians are not being taught enough biology. The need for interdisciplinary curricula that includes disciplines such as biology, physical science, and mathematics is widely recognized, but has not been widely implemented. In this paper, it is suggested that students develop a skill set of ecology, mathematics and technology to encourage working across disciplinary boundaries. To illustrate such a skill set, a predator-prey model that contains self-limiting factors for both predator and prey is suggested. The general idea of dynamics, is introduced and students are encouraged to discover the applicability of this approach to more complex biological systems. The level of mathematics and technology required is not advanced; therefore, it is ideal for inclusion in a senior-level or introductory graduate-level course for students interested in mathematical biology.

Biological materials by design.

PubMed

Qin, Zhao; Dimas, Leon; Adler, David; Bratzel, Graham; Buehler, Markus J

2014-02-19

In this topical review we discuss recent advances in the use of physical insight into the way biological materials function, to design novel engineered materials 'from scratch', or from the level of fundamental building blocks upwards and by using computational multiscale methods that link chemistry to material function. We present studies that connect advances in multiscale hierarchical material structuring with material synthesis and testing, review case studies of wood and other biological materials, and illustrate how engineered fiber composites and bulk materials are designed, modeled, and then synthesized and tested experimentally. The integration of experiment and simulation in multiscale design opens new avenues to explore the physics of materials from a fundamental perspective, and using complementary strengths from models and empirical techniques. Recent developments in this field illustrate a new paradigm by which complex material functionality is achieved through hierarchical structuring in spite of simple material constituents.

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

PubMed Central

Rossin, Elizabeth J.; Lage, Kasper; Raychaudhuri, Soumya; Xavier, Ramnik J.; Tatar, Diana; Benita, Yair

2011-01-01

Genome-wide association studies (GWAS) have defined over 150 genomic regions unequivocally containing variation predisposing to immune-mediated disease. Inferring disease biology from these observations, however, hinges on our ability to discover the molecular processes being perturbed by these risk variants. It has previously been observed that different genes harboring causal mutations for the same Mendelian disease often physically interact. We sought to evaluate the degree to which this is true of genes within strongly associated loci in complex disease. Using sets of loci defined in rheumatoid arthritis (RA) and Crohn's disease (CD) GWAS, we build protein–protein interaction (PPI) networks for genes within associated loci and find abundant physical interactions between protein products of associated genes. We apply multiple permutation approaches to show that these networks are more densely connected than chance expectation. To confirm biological relevance, we show that the components of the networks tend to be expressed in similar tissues relevant to the phenotypes in question, suggesting the network indicates common underlying processes perturbed by risk loci. Furthermore, we show that the RA and CD networks have predictive power by demonstrating that proteins in these networks, not encoded in the confirmed list of disease associated loci, are significantly enriched for association to the phenotypes in question in extended GWAS analysis. Finally, we test our method in 3 non-immune traits to assess its applicability to complex traits in general. We find that genes in loci associated to height and lipid levels assemble into significantly connected networks but did not detect excess connectivity among Type 2 Diabetes (T2D) loci beyond chance. Taken together, our results constitute evidence that, for many of the complex diseases studied here, common genetic associations implicate regions encoding proteins that physically interact in a preferential manner, in line with observations in Mendelian disease. PMID:21249183

Biomorphodynamics: Physical-biological feedbacks that shape landscapes

USGS Publications Warehouse

Murray, A.B.; Knaapen, M.A.F.; Tal, M.; Kirwan, M.L.

2008-01-01

Plants and animals affect morphological evolution in many environments. The term "ecogeomorphology" describes studies that address such effects. In this opinion article we use the term "biomorphodynamics" to characterize a subset of ecogeomorphologic studies: those that investigate not only the effects of organisms on physical processes and morphology but also how the biological processes depend on morphology and physical forcing. The two-way coupling precipitates feedbacks, leading to interesting modes of behavior, much like the coupling between flow/sediment transport and morphology leads to rich morphodynamic behaviors. Select examples illustrate how even the basic aspects of some systems cannot be understood without considering biomorphodynamic coupling. Prominent examples include the dynamic interactions between vegetation and flow/sediment transport that can determine river channel patterns and the multifaceted biomorphodynamic feedbacks shaping tidal marshes and channel networks. These examples suggest that the effects of morphology and physical processes on biology tend to operate over the timescale of the evolution of the morphological pattern. Thus, in field studies, which represent a snapshot in the pattern evolution, these effects are often not as obvious as the effects of biology on physical processes. However, numerical modeling indicates that the influences on biology from physical processes can play a key role in shaping landscapes and that even local and temporary vegetation disturbances can steer large-scale, long-term landscape evolution. The prevalence of biomorphodynamic research is burgeoning in recent years, driven by societal need and a confluence of complex systems-inspired modeling approaches in ecology and geomorphology. To make fundamental progress in understanding the dynamics of many landscapes, our community needs to increasingly learn to look for two-way, biomorphodynamic feedbacks and to collect new types of data to support the modeling of such emergent interactions. Copyright 2008 by the American Geophysical Union.

Interdisciplinary and physics challenges of network theory

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra

2015-09-01

Network theory has unveiled the underlying structure of complex systems such as the Internet or the biological networks in the cell. It has identified universal properties of complex networks, and the interplay between their structure and dynamics. After almost twenty years of the field, new challenges lie ahead. These challenges concern the multilayer structure of most of the networks, the formulation of a network geometry and topology, and the development of a quantum theory of networks. Making progress on these aspects of network theory can open new venues to address interdisciplinary and physics challenges including progress on brain dynamics, new insights into quantum technologies, and quantum gravity.

Phase from defocus

NASA Astrophysics Data System (ADS)

Mandula, Ondrej; Allier, Cédric; Hervé, Lionel; Denarier, Eric; Fourest-Lieuvin, Anne; Gory-Fauré, Sylvie; Vinit, Angélique; Morales, Sophie

2018-02-01

We present a simple and compact phase imaging microscope for long-term observation of non-absorbing biological samples such as unstained cells in nutritive media. The phase image is obtained from a single defocused image taken with a standard wide-field microscope. Using a semi-coherent light source allows us to computationally re-focus image post-acquisition and recover both phase and transmission of the complex specimen. The simplicity of the system reduces both the cost and its physical size and allows a long-term observation of samples directly in a standard biological incubator. The low cost of the system can contribute to the democratization of science by allowing to perform complex long-term biological experiments to the laboratories with constrained budget. In this proceeding we present several results taken with our prototype and discuss the possibilities and limitations of our system.

Equivalent formulations of “the equation of life”

NASA Astrophysics Data System (ADS)

Ao, Ping

2014-07-01

Motivated by progress in theoretical biology a recent proposal on a general and quantitative dynamical framework for nonequilibrium processes and dynamics of complex systems is briefly reviewed. It is nothing but the evolutionary process discovered by Charles Darwin and Alfred Wallace. Such general and structured dynamics may be tentatively named “the equation of life”. Three equivalent formulations are discussed, and it is also pointed out that such a quantitative dynamical framework leads naturally to the powerful Boltzmann-Gibbs distribution and the second law in physics. In this way, the equation of life provides a logically consistent foundation for thermodynamics. This view clarifies a particular outstanding problem and further suggests a unifying principle for physics and biology.

OBPR Product Lines, Human Research Initiative, and Physics Roadmap for Exploration

NASA Technical Reports Server (NTRS)

Israelsson, Ulf

2004-01-01

The pace of change has increased at NASA. OBPR s focus is now on the Human interface as it relates to the new Exploration vision. The fundamental physics community must demonstrate how we can contribute. Many opportunities exist for physicists to participate in addressing NASA's cross-disciplinary exploration challenges: a) Physicists can contribute to elucidating basic operating principles for complex biological systems; b) Physics technologies can contribute to developing miniature sensors and systems required for manned missions to Mars. NASA Codes other than OBPR may be viable sources of funding for physics research.

Pubertal Timing and Adolescent Sexual Behavior in Girls

ERIC Educational Resources Information Center

Moore, Sarah R.; Harden, K. Paige; Mendle, Jane

2014-01-01

Girls who experience earlier pubertal timing relative to peers also exhibit earlier timing of sexual intercourse and more unstable sexual relationships. Although pubertal development initiates feelings of physical desire, the transition into romantic and sexual relationships involves complex biological and social processes contributing both to…

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

DOE PAGES

Harrison, Jesse P.; Berry, David

2017-04-13

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrison, Jesse P.; Berry, David

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Managing bioengineering complexity with AI techniques.

PubMed

Beal, Jacob; Adler, Aaron; Yaman, Fusun

2016-10-01

Our capabilities for systematic design and engineering of biological systems are rapidly increasing. Effectively engineering such systems, however, requires the synthesis of a rapidly expanding and changing complex body of knowledge, protocols, and methodologies. Many of the problems in managing this complexity, however, appear susceptible to being addressed by artificial intelligence (AI) techniques, i.e., methods enabling computers to represent, acquire, and employ knowledge. Such methods can be employed to automate physical and informational "routine" work and thus better allow humans to focus their attention on the deeper scientific and engineering issues. This paper examines the potential impact of AI on the engineering of biological organisms through the lens of a typical organism engineering workflow. We identify a number of key opportunities for significant impact, as well as challenges that must be overcome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Chapter 5: Thermal Indices and Their Applications for Livestock Environments

USDA-ARS?s Scientific Manuscript database

Heat exchanges with the environment are a crucial process for maintaining homeothermy by humans and other animals. These exchanges involve heat production, conservation and dissipation, and are dependent on both biological and physical factors. The complexity of these exchanges has led to many attem...

Soils, peatlands, and biomonitoring

Treesearch

James Doolittle

2009-01-01

Soils are three-dimensional (3D) natural bodies conSlStmg of unconsolidated mineral and organic materials that form a continuous blanket over most of the earth's land sUlface. At all sca les of measurements, soils are exceedingly complex and variable in biological, chemical, physical, mineralogical, and electromagnetic properties....

Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.

PubMed

Hulme, S Elizabeth; Whitesides, George M

2011-05-16

This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (<1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools-biological, chemical, and physical-that are available to researchers studying the worm. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mathematics, structuralism and biology.

PubMed

Saunders, P T

1988-01-01

A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.

Mechanistic understanding of nanoparticles' interactions with extracellular matrix: the cell and immune system.

PubMed

Engin, Ayse Basak; Nikitovic, Dragana; Neagu, Monica; Henrich-Noack, Petra; Docea, Anca Oana; Shtilman, Mikhail I; Golokhvast, Kirill; Tsatsakis, Aristidis M

2017-06-24

Extracellular matrix (ECM) is an extraordinarily complex and unique meshwork composed of structural proteins and glycosaminoglycans. The ECM provides essential physical scaffolding for the cellular constituents, as well as contributes to crucial biochemical signaling. Importantly, ECM is an indispensable part of all biological barriers and substantially modulates the interchange of the nanotechnology products through these barriers. The interactions of the ECM with nanoparticles (NPs) depend on the morphological characteristics of intercellular matrix and on the physical characteristics of the NPs and may be either deleterious or beneficial. Importantly, an altered expression of ECM molecules ultimately affects all biological processes including inflammation. This review critically discusses the specific behavior of NPs that are within the ECM domain, and passing through the biological barriers. Furthermore, regenerative and toxicological aspects of nanomaterials are debated in terms of the immune cells-NPs interactions.

C. elegans network biology: a beginning.

PubMed Central

Piano, Fabio; Gunsalus, Kristin C; Hill, David E; Vidal, Marc

2006-01-01

The architecture and dynamics of molecular networks can provide an understanding of complex biological processes complementary to that obtained from the in-depth study of single genes and proteins. With a completely sequenced and well-annotated genome, a fully characterized cell lineage, and powerful tools available to dissect development, Caenorhabditis elegans, among metazoans, provides an optimal system to bridge cellular and organismal biology with the global properties of macromolecular networks. This chapter considers omic technologies available for C. elegans to describe molecular networks--encompassing transcriptional and phenotypic profiling as well as physical interaction mapping--and discusses how their individual and integrated applications are paving the way for a network-level understanding of C. elegans biology. PMID:18050437

Natural selection and self-organization in complex adaptive systems.

PubMed

Di Bernardo, Mirko

2010-01-01

The central theme of this work is self-organization "interpreted" both from the point of view of theoretical biology, and from a philosophical point of view. By analysing, on the one hand, those which are now considered--not only in the field of physics--some of the most important discoveries, that is complex systems and deterministic chaos and, on the other hand, the new frontiers of systemic biology, this work highlights how large thermodynamic systems which are open can spontaneously stay in an orderly regime. Such systems can represent the natural source of the order required for a stable self-organization, for homoeostasis and for hereditary variations. The order, emerging in enormous randomly interconnected nets of binary variables, is almost certainly only the precursor of similar orders emerging in all the varieties of complex systems. Hence, this work, by finding new foundations for the order pervading the living world, advances the daring hypothesis according to which Darwinian natural selection is not the only source of order in the biosphere. Thus, the article, by examining the passage from Prigogine's dissipative structures theory to the contemporary theory of biological complexity, highlights the development of a coherent and continuous line of research which is set to individuate the general principles marking the profound reality of that mysterious self-organization characterizing the complexity of life.

Editorial Commentary: Paving a Road Requires a Well-Mixed Cement Stem Cells, Platelet-Rich Plasma, and Shoulder Rotator Cuff Healing.

PubMed

Maffulli, Nicola

2018-03-01

The process of healing in musculoskeletal tissues is complex, and the addition of devices, including platelet-rich plasma and mesenchymal stem cells, to biologically enhance it may favor its optimization. This work shows in a compelling fashion that it is possible to produce the right admixture of physical and biological factors to make it happen in rotator cuff repair. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Physical Principles of Development of the State Standard of Biological Cell Polarizability

NASA Astrophysics Data System (ADS)

Shuvalov, G. V.; Generalov, K. V.; Generalov, V. M.; Kruchinina, M. V.; Koptev, E. S.; Minin, O. V.; Minin, I. V.

2018-03-01

A new state standard of biological cell polarizability based on micron-size latex particles has been developed. As a standard material, it is suggested to use polystyrene. Values of the polarizability calculated for erythrocytes and values of the polarizability of micron-size spherical latex particles measured with measuring-computing complexes agree within the limits of satisfactory relative error. The Standard allows one the unit of polarizability measurements [m3] to be assigned to cells and erythrocytes for the needs of medicine.

Optical radiation measurements: instrumentation and sources of error.

PubMed

Landry, R J; Andersen, F A

1982-07-01

Accurate measurement of optical radiation is required when sources of this radiation are used in biological research. The most difficult measurements of broadband noncoherent optical radiations usually must be performed by a highly trained specialist using sophisticated, complex, and expensive instruments. Presentation of the results of such measurement requires correct use of quantities and units with which many biological researchers are unfamiliar. The measurement process, physical quantities and units, measurement systems with instruments, and sources of error and uncertainties associated with optical radiation measurements are reviewed.

Biology of Nanobots

NASA Astrophysics Data System (ADS)

Duan, Wentao; Pavlick, Ryan; Sen, Ayusman

2013-12-01

One of the more interesting recent discoveries has been the ability to design nano/microbots which catalytically harness the chemical energy in their environment to move autonomously. Their potential applications include delivery of materials, self-assembly of superstructures, and roving sensors. One emergent area of research is the study of their collective behavior and how they emulate living systems. The aim of this chapter is to describe the "biology" of nanobots, summarizing the fundamentals physics behind their motion and how the bots interact with each other to initiate complex emergent behavior.

Science, Semantics, and Social Change.

ERIC Educational Resources Information Center

Lemke, J. L.

Social semiotics suggests that social and cultural formations, including the language and practice of science and the ways in which new generations and communities advance them, develop as an integral part of the evolution of social ecosystems. Some recent models of complex dynamic systems in physics, chemistry, and biology focus more on the…

Thermodynamical Arguments against Evolution

ERIC Educational Resources Information Center

Rosenhouse, Jason

2017-01-01

The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be…

Book Review: "The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface, Second Edition"

USDA-ARS?s Scientific Manuscript database

The complexity of the biological, chemical, and physical interactions occurring in the volume of soil surrounding the root of a growing plant dictates that a multidisciplinary approach must be taken to improve our understanding of this rhizosphere. Hence, "The Rhizosphere: Biochemistry and Organic S...

Learning Complex Scientific Information: Motivation Theory and Its Relation to Student Perceptions.

ERIC Educational Resources Information Center

Hynd, Cynthia; Holschuh, Jodi; Nist, Sherrie

2000-01-01

Examines motivation in high school students' conceptual change about physics principles, and college students' motivation for biology learning. Finds grades and interest were important, but students did not report the importance of social support. Suggests similar motivations are important in both conceptual change and assimilation and help…

PREFACE: 3rd International Workshop on Statistical Physics and Mathematics for Complex Systems (SPMCS 2012)

NASA Astrophysics Data System (ADS)

Tayurskii, Dmitrii; Abe, Sumiyoshi; Alexandre Wang, Q.

2012-11-01

The 3rd International Workshop on Statistical Physics and Mathematics for Complex Systems (SPMCS2012) was held between 25-30 August at Kazan (Volga Region) Federal University, Kazan, Russian Federation. This workshop was jointly organized by Kazan Federal University and Institut Supérieur des Matériaux et Mécaniques Avancées (ISMANS), France. The series of SPMCS workshops was created in 2008 with the aim to be an interdisciplinary incubator for the worldwide exchange of innovative ideas and information about the latest results. The first workshop was held at ISMANS, Le Mans (France) in 2008, and the third at Huazhong Normal University, Wuhan (China) in 2010. At SPMCS2012, we wished to bring together a broad community of researchers from the different branches of the rapidly developing complexity science to discuss the fundamental theoretical challenges (geometry/topology, number theory, statistical physics, dynamical systems, etc) as well as experimental and applied aspects of many practical problems (condensed matter, disordered systems, financial markets, chemistry, biology, geoscience, etc). The program of SPMCS2012 was prepared based on three categories: (i) physical and mathematical studies (quantum mechanics, generalized nonequilibrium thermodynamics, nonlinear dynamics, condensed matter physics, nanoscience); (ii) natural complex systems (physical, geophysical, chemical and biological); (iii) social, economical, political agent systems and man-made complex systems. The conference attracted 64 participants from 10 countries. There were 10 invited lectures, 12 invited talks and 28 regular oral talks in the morning and afternoon sessions. The book of Abstracts is available from the conference website (http://www.ksu.ru/conf/spmcs2012/?id=3). A round table was also held, the topic of which was 'Recent and Anticipated Future Progress in Science of Complexity', discussing a variety of questions and opinions important for the understanding of the concept of complexity itself, the behaviours of complex systems as well as for the finding of new theoretical methods. The papers submitted to this volume were carefully reviewed by referees. We are very grateful to the referees for their very efficient and thoughtful actions. A few submitted papers were unfortunately not included based on the referee reports. As a result, 34 papers are included here. We are very grateful to the members of the international advisory committee for their recommendations of speakers for SPMCS2012. We also appreciate the behind-the-scenes work of the members of the local organizing committee in preparing the conference site, web page, mail correspondence, arrangements for excursions and accommodation, handling the financial support for participants, and so on. Finally, we acknowledge the support from Kazan Federal University. Sumiyoshi Abe Alain Le Méhauté Dmitrii Tayurskii

A systems biology approach to studying Tai Chi, physiological complexity and healthy aging: design and rationale of a pragmatic randomized controlled trial.

PubMed

Wayne, Peter M; Manor, Brad; Novak, Vera; Costa, Madelena D; Hausdorff, Jeffrey M; Goldberger, Ary L; Ahn, Andrew C; Yeh, Gloria Y; Peng, C-K; Lough, Matthew; Davis, Roger B; Quilty, Mary T; Lipsitz, Lewis A

2013-01-01

Aging is typically associated with progressive multi-system impairment that leads to decreased physical and cognitive function and reduced adaptability to stress. Due to its capacity to characterize complex dynamics within and between physiological systems, the emerging field of complex systems biology and its array of quantitative tools show great promise for improving our understanding of aging, monitoring senescence, and providing biomarkers for evaluating novel interventions, including promising mind-body exercises, that treat age-related disease and promote healthy aging. An ongoing, two-arm randomized clinical trial is evaluating the potential of Tai Chi mind-body exercise to attenuate age-related loss of complexity. A total of 60 Tai Chi-naïve healthy older adults (aged 50-79) are being randomized to either six months of Tai Chi training (n=30), or to a waitlist control receiving unaltered usual medical care (n=30). Our primary outcomes are complexity-based measures of heart rate, standing postural sway and gait stride interval dynamics assessed at 3 and 6months. Multiscale entropy and detrended fluctuation analysis are used as entropy- and fractal-based measures of complexity, respectively. Secondary outcomes include measures of physical and psychological function and tests of physiological adaptability also assessed at 3 and 6months. Results of this study may lead to novel biomarkers that help us monitor and understand the physiological processes of aging and explore the potential benefits of Tai Chi and related mind-body exercises for healthy aging. Copyright © 2012 Elsevier Inc. All rights reserved.

A morphospace for synthetic organs and organoids: the possible and the actual.

PubMed

Ollé-Vila, Aina; Duran-Nebreda, Salva; Conde-Pueyo, Núria; Montañez, Raúl; Solé, Ricard

2016-04-18

Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.

The physical and biological basis of quantitative parameters derived from diffusion MRI

PubMed Central

2012-01-01

Diffusion magnetic resonance imaging is a quantitative imaging technique that measures the underlying molecular diffusion of protons. Diffusion-weighted imaging (DWI) quantifies the apparent diffusion coefficient (ADC) which was first used to detect early ischemic stroke. However this does not take account of the directional dependence of diffusion seen in biological systems (anisotropy). Diffusion tensor imaging (DTI) provides a mathematical model of diffusion anisotropy and is widely used. Parameters, including fractional anisotropy (FA), mean diffusivity (MD), parallel and perpendicular diffusivity can be derived to provide sensitive, but non-specific, measures of altered tissue structure. They are typically assessed in clinical studies by voxel-based or region-of-interest based analyses. The increasing recognition of the limitations of the diffusion tensor model has led to more complex multi-compartment models such as CHARMED, AxCaliber or NODDI being developed to estimate microstructural parameters including axonal diameter, axonal density and fiber orientations. However these are not yet in routine clinical use due to lengthy acquisition times. In this review, I discuss how molecular diffusion may be measured using diffusion MRI, the biological and physical bases for the parameters derived from DWI and DTI, how these are used in clinical studies and the prospect of more complex tissue models providing helpful micro-structural information. PMID:23289085

Contrasting ENSO types with novel satellite derived ocean phytoplankton biomass

NASA Astrophysics Data System (ADS)

Sharma, P.; Singh, A. M.; Marinov, I.; Kostadinov, T. S.

2016-12-01

Observed variations in community structure and biogeochemical processes in the tropics and the North Atlantic have been linked, in the first order, to the El Niño Southern Oscillation phenomenon (e.g., Bates, 2001; Karl et al., 2001; Di Lorenzo et al., 2010; Di Lorenzo et al., 2013). Current significant technical advances have allowed for the retrieval of biological data from the optical properties of the water via satellite ocean color remote sensing, providing an opportunity for quantifying the relationships between biological and climate indices. Studies have focused in-depth on contrasting flavors of the ENSO types with various physical (e.g., Singh et al. 2011; Turk et al. 2011) and biological (e.g., Radenac et al. 2012) indices. Here, we analyze the impact of different ENSO types on biology via analysis of recently-derived backscattering-based biomass separated into size-groups (Kostadinov et al. 2010, 2016) over the 17-year (1997-2013). We further contrast the responses of biomass with those of chlorophyll (Chl) and particulate inorganic carbon (PIC). We analyze the complex spatial differences in both physical (SST, mixed layer depth, winds) and biological (Chl, total and size-partitioned biomass) variability across the Pacific warm pool and equatorial tongue via simple EOF, combined regression-EOF and Agglomerative Hierarchical Clustering (AHC) analysis. The interannual variability in the physical and biological fields show clear signatures of the Niño cold-tongue (NCT) and Niño warm pool (NWP). Possible mechanisms responsible for these signatures are discussed.

Models of chromatin spatial organisation in the cell nucleus

NASA Astrophysics Data System (ADS)

Nicodemi, Mario

2014-03-01

In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Recent experiments have started unveiling the interaction map of DNA sites genome-wide, revealing different levels of organisation at different scales. The principles, though, which orchestrate such a complex 3D structure remain still mysterious. I will overview the scenario emerging from some classical polymer physics models of the general aspect of chromatin spatial organisation. The available experimental data, which can be rationalised in a single framework, support a picture where chromatin is a complex mixture of differently folded regions, self-organised across spatial scales according to basic physical mechanisms. I will also discuss applications to specific DNA loci, e.g. the HoxB locus, where models informed with biological details, and tested against targeted experiments, can help identifying the determinants of folding.

Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.

PubMed

Nariai, N; Kim, S; Imoto, S; Miyano, S

2004-01-01

We propose a statistical method to estimate gene networks from DNA microarray data and protein-protein interactions. Because physical interactions between proteins or multiprotein complexes are likely to regulate biological processes, using only mRNA expression data is not sufficient for estimating a gene network accurately. Our method adds knowledge about protein-protein interactions to the estimation method of gene networks under a Bayesian statistical framework. In the estimated gene network, a protein complex is modeled as a virtual node based on principal component analysis. We show the effectiveness of the proposed method through the analysis of Saccharomyces cerevisiae cell cycle data. The proposed method improves the accuracy of the estimated gene networks, and successfully identifies some biological facts.

Transforming Better Babies into Fitter Families: archival resources and the history of American eugenics movement, 1908-1930.

PubMed

Selden, Steven

2005-06-01

In the early 1920s, determinist conceptions of biology helped to transform Better Babies contest into Fitter Families competitions with a strong commitment to controlled human breeding. While the earlier competitions were concerned for physical and mental standards, the latter contests collected data on a broad range of presumed hereditary characters. The complex behaviors thought to be determined by one's heredity included being generous, jealous, and cruel. In today's context, the popular media often interpret advances in molecular genetics in a similarly reductive and determinist fashion. This paper argues that such a narrow interpretation of contemporary biology unnecessarily constrains the public in developing social policies concerning complex social behavior ranging from crime to intelligence.

Patients’ conceptions of their own influence on good treatment response to biological therapy in chronic inflammatory arthritis

PubMed Central

Larsson, Ingrid

2017-01-01

Background Biological therapies are common in the treatment of patients with chronic inflammatory arthritis (CIA). However, despite the fact that many patients respond well to their biological therapies, there are still a number of nonresponders. In order to design the best care for patients, it is important to understand how they conceive their own role in their treatment response. Objective To explore how patients with CIA conceive their own influence on a good treatment response to biological therapy. Methods This study had an exploratory and descriptive design with a phenomenographic approach. Interviews were conducted with 25 patients (11 women and 14 men) aged 17–79 years, with CIA who were undergoing biological therapy and who had low disease activity or were in remission. Results Patients with CIA undergoing biological therapy conceived their own influence on good treatment response in terms of adherence, physical activity, mental attitude, social support, and self-awareness. Adherence was described as the foundation for the patients’ own influence on good treatment response. Physical activity, mental attitude, and social support reflected three essential ways of understanding patients’ influence on good treatment response where the patients spoke about physical strength, mental strength, and social strength. Self-awareness reflected a comprehensive way of influencing good treatment response in which patients balanced their physical, mental, and social resources in partnership with health care professionals. Conclusion Patients conceived that they had a responsibility for adhering to the treatment as well as achieving balance in life in order to ensure good treatment response. Self-awareness was essential for maintaining a good treatment response, and this reflected the patients’ awareness of the complexity of living their lives with a chronic illness. PMID:28706444

Patients' conceptions of their own influence on good treatment response to biological therapy in chronic inflammatory arthritis.

PubMed

Larsson, Ingrid

2017-01-01

Biological therapies are common in the treatment of patients with chronic inflammatory arthritis (CIA). However, despite the fact that many patients respond well to their biological therapies, there are still a number of nonresponders. In order to design the best care for patients, it is important to understand how they conceive their own role in their treatment response. To explore how patients with CIA conceive their own influence on a good treatment response to biological therapy. This study had an exploratory and descriptive design with a phenomenographic approach. Interviews were conducted with 25 patients (11 women and 14 men) aged 17-79 years, with CIA who were undergoing biological therapy and who had low disease activity or were in remission. Patients with CIA undergoing biological therapy conceived their own influence on good treatment response in terms of adherence, physical activity, mental attitude, social support, and self-awareness. Adherence was described as the foundation for the patients' own influence on good treatment response. Physical activity, mental attitude, and social support reflected three essential ways of understanding patients' influence on good treatment response where the patients spoke about physical strength, mental strength, and social strength. Self-awareness reflected a comprehensive way of influencing good treatment response in which patients balanced their physical, mental, and social resources in partnership with health care professionals. Patients conceived that they had a responsibility for adhering to the treatment as well as achieving balance in life in order to ensure good treatment response. Self-awareness was essential for maintaining a good treatment response, and this reflected the patients' awareness of the complexity of living their lives with a chronic illness.

Physics and Its Interfaces with Medicinal Chemistry and Drug Design

NASA Astrophysics Data System (ADS)

Santos, Ricardo N.; Andricopulo, Adriano D.

2013-08-01

Medicinal chemistry is a multidisciplinary subject that integrates knowledge from a variety of fields of science, including, but not limited to, chemistry, biology, and physics. The area of drug design involves the cooperative work of scientists with a diverse range of backgrounds and technical skills, trying to tackle complex problems using an integration of approaches and methods. One important contribution to this field comes from physics through studies that attempt to identify and quantify the molecular interactions between small molecules (drugs) and biological targets (receptors), such as the forces that govern the interactions, the thermodynamics of the drug-receptor interactions, and so on. In this context, the interfaces of physics, medicinal chemistry, and drug design are of vital importance for the development of drugs that not only have the right chemistry but also the right intermolecular properties to interact at the macromolecular level, providing useful information about the principles and molecular mechanisms underlying the therapeutic action of drugs. This article highlights some of the most important connections between physics and medicinal chemistry in the design of new drugs.

Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context.

PubMed

Werner, Marco; Auth, Thorsten; Beales, Paul A; Fleury, Jean Baptiste; Höök, Fredrik; Kress, Holger; Van Lehn, Reid C; Müller, Marcus; Petrov, Eugene P; Sarkisov, Lev; Sommer, Jens-Uwe; Baulin, Vladimir A

2018-04-03

Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and the alteration of biological function. Nature and humans use different design strategies to create nanomaterials: biological objects have emerged from billions of years of evolution and from adaptation to their environment resulting in high levels of structural complexity; in contrast, synthetic nanomaterials result from minimalistic but controlled design options limited by the authors' current understanding of the biological world. This conceptual mismatch makes it challenging to create synthetic nanomaterials that possess desired functions in biological media. In many biologically relevant applications, nanomaterials must enter the cell interior to perform their functions. An essential transport barrier is the cell-protecting plasma membrane and hence the understanding of its interaction with nanomaterials is a fundamental task in biotechnology. The authors present open questions in the field of nanomaterial interactions with biological membranes, including: how physical mechanisms and molecular forces acting at the nanoscale restrict or inspire design options; which levels of complexity to include next in computational and experimental models to describe how nanomaterials cross barriers via passive or active processes; and how the biological media and protein corona interfere with nanomaterial functionality. In this Perspective, the authors address these questions with the aim of offering guidelines for the development of next-generation nanomaterials that function in biological media.

Biosynthetic inorganic chemistry.

PubMed

Lu, Yi

2006-08-25

Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.

Complex Plasma Physics and Rising Above the Gathering Storm

NASA Astrophysics Data System (ADS)

Hyde, Truell

2008-11-01

Research in complex plasma is prevalent across a variety of regimes ranging from the majority of plasma processing environments to many astrophysical settings. Dust particles suspended within such plasmas acquire a charge from collisions with electrons and ions in the plasma. Depending upon the ratio of their interparticle potential energy to their average kinetic energy, once charged these particles can form a gaseous, liquid or crystalline structure with short to longer range ordering. The field of complex plasmas thus offers research opportunities across a wide range of academic disciplines including physics, chemistry, biology, mathematics, electrical engineering and nanoscience. The field of complex plasmas also offers unique educational research opportunities for combating many of the issues raised in Rising Above the Gathering Storm, recently published by the National Academies Press. CASPER's Educational Outreach programs, supported by the National Science Foundation, the Department of Education and the Department of Labor takes advantage of these opportunities through a variety of avenues including a REU / RET program, a High School Scholars Program, integrated curriculum development and the CASPER Physics Circus. Together, these programs impact thousands of students and parents while providing K-12 teachers with curriculum, supporting hands-on material and support for introducing plasma and basic physical science concepts into the classroom. Both research results and educational outreach concepts from the above will be discussed.

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

PubMed Central

Koorehdavoudi, Hana; Bogdan, Paul

2016-01-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity. PMID:27297496

A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions

NASA Astrophysics Data System (ADS)

Koorehdavoudi, Hana; Bogdan, Paul

2016-06-01

Biological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group of N agents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.

From Random Walks to Brownian Motion, from Diffusion to Entropy: Statistical Principles in Introductory Physics

NASA Astrophysics Data System (ADS)

Reeves, Mark

2014-03-01

Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is dominant contribution of the entropy in driving important biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy) that enable students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce seemingly complex biological processes and structures to be described by tractable models that include deterministic processes and simple probabilistic inference. The students test these models in simulations and in laboratory experiments that are biologically relevant. The students are challenged to bridge the gap between statistical parameterization of their data (mean and standard deviation) and simple model-building by inference. This allows the students to quantitatively describe realistic cellular processes such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront ``random'' forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory physics with a bio focus. Supported by NSF DUE.

A new universality class in corpus of texts; A statistical physics study

NASA Astrophysics Data System (ADS)

Najafi, Elham; Darooneh, Amir H.

2018-05-01

Text can be regarded as a complex system. There are some methods in statistical physics which can be used to study this system. In this work, by means of statistical physics methods, we reveal new universal behaviors of texts associating with the fractality values of words in a text. The fractality measure indicates the importance of words in a text by considering distribution pattern of words throughout the text. We observed a power law relation between fractality of text and vocabulary size for texts and corpora. We also observed this behavior in studying biological data.

Brain reserve hypothesis in dementia.

PubMed

Fratiglioni, Laura; Wang, Hui-Xin

2007-08-01

The concept of brain reserve refers to the ability to tolerate the age-related changes and the disease related pathology in the brain without developing clear clinical symptoms or signs. A considerable body of biological research has documented that a number of factors including education, work complexity, social network, and leisure activities may contribute to this reserve allowing cognitive function to be maintained in old ages. Epidemiological studies have also related these factors to the development of dementia, suggesting that intellectual challenges experienced across the whole life span may increase the brain reserve and be crucial for the occurrence of dementia symptoms in late life. This paper is a systematic review of the published epidemiological studies on this topic. The availability of numerous epidemiological and biological data investigating the reserve hypothesis in dementia permits some preliminary conclusions. High education, adult-life occupational work complexity, as well as a mentally and socially integrated lifestyle in late life could postpone the onset of clinical dementia and AD. The relevance of physical activity itself remains in debate, as most physical activities include also social and mental stimulation. Leisure activities with all three components--physical, mental and social--seem to have the most beneficial effect. Delaying dementia onset by five years would halve dementia prevalence and substantially decrease the number of dementia cases in the community.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elber, Ron

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.

Faking It Won't Make It in Science

ERIC Educational Resources Information Center

Cavanagh, Sean

2004-01-01

For years, educators and researchers have seen teachers at all grade levels attempt to upgrade their grasp of physics, chemistry, and biology, from basic theories to complex material. Now, the pressure on schools and instructors to improve science instruction is likely to intensify, with approaching federal requirements on states to test students…

Evidence for polyphosphate accumulating organism (PAO)-mediated phosphorus cycling in stream biofilms under alternating aerobic/anaerobic conditions

USDA-ARS?s Scientific Manuscript database

Phosphorus (P) is often a limiting nutrient in freshwater ecosystems and excessive inputs can lead to eutrophication. In-stream cycling of P involves complex biological, chemical, and physical processes that are not fully understood. Microbial metabolisms are suspected to control oxygen-dependent up...

Integrative approaches to investigating human-natural systems: the Baltimore ecosystem study

Treesearch

Mary L. Cadenasso; Steward T.A. Pickett; Morgan J. Grove; Morgan J. Grove

2006-01-01

This paper presents an overview of the research approaches used to study metropolitan Baltimore (Maryland, USA) as an ecological system. The urban ecosystem is a complex of biophysical, social, and built components, and is studied by an interdisciplinary teamof biological, social, and physical scientists, and urban designers. Ecology ?of? themetropolis is addressed...

Assessment of electrical conductivity as a surrogate measurement for water samples in a tracer injection experiment

USDA-ARS?s Scientific Manuscript database

The transport behavior of solutes in streams depends on chemical, physical, biological, and hydrodynamic processes. Although it is a very complex system, it is known that this behavior is greatly influenced by surface and subsurface flows. For this reason, tracer injection in the water flows is one ...

Restoring and Maintaining Riparian Habitat on Private Pastureland

Treesearch

Nancy Reichard

1989-01-01

Protecting riparian habitat from livestock grazing on private land is a complex task that requires paying attention to sociological and economic as well as physical and biological factors. Six livestock exclusion fencing projects on private property in northwestern California are described. The importance of long term maintenance and the need for landowner incentives...

Body Structure and Physical Self-Concept in Early Adolescence

ERIC Educational Resources Information Center

Zsakai, Annamaria; Karkus, Zsolt; Utczas, Katinka; Bodzsar, Eva B.

2017-01-01

In adolescence, the complexity of human ontogenesis embraces biological growth and maturation as well as mental, affective, and cognitive progress, and adaptation to the requirements of society. To accept our morphological constellation as part of our gender may prove a problem even to a child of average rate of maturation. The main purposes of…

Biological mechanisms underlying the role of physical fitness in health and resilience

PubMed Central

Silverman, Marni N.; Deuster, Patricia A.

2014-01-01

Physical fitness, achieved through regular exercise and/or spontaneous physical activity, confers resilience by inducing positive psychological and physiological benefits, blunting stress reactivity, protecting against potentially adverse behavioural and metabolic consequences of stressful events and preventing many chronic diseases. In this review, we discuss the biological mechanisms underlying the beneficial effects of physical fitness on mental and physical health. Physical fitness appears to buffer against stress-related disease owing to its blunting/optimizing effects on hormonal stress responsive systems, such as the hypothalamic–pituitary–adrenal axis and the sympathetic nervous system. This blunting appears to contribute to reduced emotional, physiological and metabolic reactivity as well as increased positive mood and well-being. Another mechanism whereby regular exercise and/or physical fitness may confer resilience is through minimizing excessive inflammation. Chronic psychological stress, physical inactivity and abdominal adiposity have been associated with persistent, systemic, low-grade inflammation and exert adverse effects on mental and physical health. The anti-inflammatory effects of regular exercise/activity can promote behavioural and metabolic resilience, and protect against various chronic diseases associated with systemic inflammation. Moreover, exercise may benefit the brain by enhancing growth factor expression and neural plasticity, thereby contributing to improved mood and cognition. In summary, the mechanisms whereby physical fitness promotes increased resilience and well-being and positive psychological and physical health are diverse and complex. PMID:25285199

Biological mechanisms underlying the role of physical fitness in health and resilience.

PubMed

Silverman, Marni N; Deuster, Patricia A

2014-10-06

Physical fitness, achieved through regular exercise and/or spontaneous physical activity, confers resilience by inducing positive psychological and physiological benefits, blunting stress reactivity, protecting against potentially adverse behavioural and metabolic consequences of stressful events and preventing many chronic diseases. In this review, we discuss the biological mechanisms underlying the beneficial effects of physical fitness on mental and physical health. Physical fitness appears to buffer against stress-related disease owing to its blunting/optimizing effects on hormonal stress responsive systems, such as the hypothalamic-pituitary-adrenal axis and the sympathetic nervous system. This blunting appears to contribute to reduced emotional, physiological and metabolic reactivity as well as increased positive mood and well-being. Another mechanism whereby regular exercise and/or physical fitness may confer resilience is through minimizing excessive inflammation. Chronic psychological stress, physical inactivity and abdominal adiposity have been associated with persistent, systemic, low-grade inflammation and exert adverse effects on mental and physical health. The anti-inflammatory effects of regular exercise/activity can promote behavioural and metabolic resilience, and protect against various chronic diseases associated with systemic inflammation. Moreover, exercise may benefit the brain by enhancing growth factor expression and neural plasticity, thereby contributing to improved mood and cognition. In summary, the mechanisms whereby physical fitness promotes increased resilience and well-being and positive psychological and physical health are diverse and complex.

Synchronisation of chaos and its applications

NASA Astrophysics Data System (ADS)

Eroglu, Deniz; Lamb, Jeroen S. W.; Pereira, Tiago

2017-07-01

Dynamical networks are important models for the behaviour of complex systems, modelling physical, biological and societal systems, including the brain, food webs, epidemic disease in populations, power grids and many other. Such dynamical networks can exhibit behaviour in which deterministic chaos, exhibiting unpredictability and disorder, coexists with synchronisation, a classical paradigm of order. We survey the main theory behind complete, generalised and phase synchronisation phenomena in simple as well as complex networks and discuss applications to secure communications, parameter estimation and the anticipation of chaos.

Final Report, 2011-2014. Forecasting Carbon Storage as Eastern Forests Age. Joining Experimental and Modeling Approaches at the UMBS AmeriFlux Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis, Peter; Bohrer, Gil; Gough, Christopher

2015-03-12

At the University of Michigan Biological Station (UMBS) AmeriFlux sites (US-UMB and US-UMd), long-term C cycling measurements and a novel ecosystem-scale experiment are revealing physical, biological, and ecological mechanisms driving long-term trajectories of C cycling, providing new data for improving modeling forecasts of C storage in eastern forests. Our findings provide support for previously untested hypotheses that stand-level structural and biological properties constrain long-term trajectories of C storage, and that remotely sensed canopy structural parameters can substantially improve model forecasts of forest C storage. Through the Forest Accelerated Succession ExperimenT (FASET), we are directly testing the hypothesis that forest Cmore » storage will increase due to increasing structural and biological complexity of the emerging tree communities. Support from this project, 2011-2014, enabled us to incorporate novel physical and ecological mechanisms into ecological, meteorological, and hydrological models to improve forecasts of future forest C storage in response to disturbance, succession, and current and long-term climate variation« less

Spatial Patterns in the Efficiency of the Biological Pump: What Controls Export Ratios at the Global Scale?

NASA Astrophysics Data System (ADS)

Moore, J. K.

2016-02-01

The efficiency of the biological pump is influenced by complex interactions between chemical, biological, and physical processes. The efficiency of export out of surface waters and down through the water column to the deep ocean has been linked to a number of factors including biota community composition, production of mineral ballast components, physical aggregation and disaggregation processes, and ocean oxygen concentrations. I will examine spatial patterns in the export ratio and the efficiency of the biological pump at the global scale using the Community Earth System Model (CESM). There are strong spatial variations in the export efficiency as simulated by the CESM, which are strongly correlated with new nutrient inputs to the euphotic zone and their impacts on phytoplankton community structure. I will compare CESM simulations that include dynamic, variable export ratios driven by the phytoplankton community structure, with simulations that impose a near-constant export ratio to examine the effects of export efficiency on nutrient and surface chlorophyll distributions. The model predicted export ratios will also be compared with recent satellite-based estimates.

Recovery of Areas Degraded by Mining Within the Amazon Forest: Interaction of the Physical Condition of Soil and Biological Activity

NASA Astrophysics Data System (ADS)

Ribeiro, A. I.; Mello, G. F.; Longo, R. M.; Fengler, F. H.; Peche Filho, A., Sr.

2017-12-01

One of the greatest natural riches of Brazil is the Amazon rainforest. The Amazon region is known for its abundance of mineral resources, and may include topaz, oil, and especially cassiterite. In this scope, the mining sector in Brazil has great strategic importance because it accounts for approximately 30% of the country's exports with a mineral production of 40 billion dollars (Brazilian Mining Institute, 2015). In this scenario, as a consequence of mining, the Amazonian ecosystem has been undergoing a constant process of degradation. An important artifice in the exploitation of mineral resources is the rehabilitation and/or recovery of degraded areas. This recovery requires the establishment of degradation indicators and also the quality of the soil associated with its biota, since the Amazonian environment is dynamic, heterogeneous and complex in its physical, chemical and biological characteristics. In this way, this work presupposes that it is possible to characterize the different stages of recovery of tillage floor areas in deactivated cassiterite mines, within the Amazonian forest, in order to evaluate the interactions between the level of biological activity (Serrapilheira Height, Coefficient Metabolic, Basal Breath) and physical soil characteristics (aggregate DMG, Porosity, Total Soil Density, Moisture Content), through canonical correlation analysis. The results present correlations between the groups of indicators. Thus, from the use of the groups defined by canonical correlations, it was possible to identify the response of the set of physical and biological variables to the areas at different stages of recovery.

Understanding the biological underpinnings of ecohydrological processes

NASA Astrophysics Data System (ADS)

Huxman, T. E.; Scott, R. L.; Barron-Gafford, G. A.; Hamerlynck, E. P.; Jenerette, D.; Tissue, D. T.; Breshears, D. D.; Saleska, S. R.

2012-12-01

Climate change presents a challenge for predicting ecosystem response, as multiple factors drive both the physical and life processes happening on the land surface and their interactions result in a complex, evolving coupled system. For example, changes in surface temperature and precipitation influence near-surface hydrology through impacts on system energy balance, affecting a range of physical processes. These changes in the salient features of the environment affect biological processes and elicit responses along the hierarchy of life (biochemistry to community composition). Many of these structural or process changes can alter patterns of soil water-use and influence land surface characteristics that affect local climate. Of the many features that affect our ability to predict the future dynamics of ecosystems, it is this hierarchical response of life that creates substantial complexity. Advances in the ability to predict or understand aspects of demography help describe thresholds in coupled ecohydrological system. Disentangling the physical and biological features that underlie land surface dynamics following disturbance are allowing a better understanding of the partitioning of water in the time-course of recovery. Better predicting the timing of phenology and key seasonal events allow for a more accurate description of the full functional response of the land surface to climate. In addition, explicitly considering the hierarchical structural features of life are helping to describe complex time-dependent behavior in ecosystems. However, despite this progress, we have yet to build an ability to fully account for the generalization of the main features of living systems into models that can describe ecohydrological processes, especially acclimation, assembly and adaptation. This is unfortunate, given that many key ecosystem services are functions of these coupled co-evolutionary processes. To date, both the lack of controlled measurements and experimentation has precluded determination of sufficient theoretical development. Understanding the land-surface response and feedback to climate change requires a mechanistic understanding of the coupling of ecological and hydrological processes and an expansion of theory from the life sciences to appropriately contribute to the broader Earth system science goal.

Oscillations and Multiple Equilibria in Microvascular Blood Flow.

PubMed

Karst, Nathaniel J; Storey, Brian D; Geddes, John B

2015-07-01

We investigate the existence of oscillatory dynamics and multiple steady-state flow rates in a network with a simple topology and in vivo microvascular blood flow constitutive laws. Unlike many previous analytic studies, we employ the most biologically relevant models of the physical properties of whole blood. Through a combination of analytic and numeric techniques, we predict in a series of two-parameter bifurcation diagrams a range of dynamical behaviors, including multiple equilibria flow configurations, simple oscillations in volumetric flow rate, and multiple coexistent limit cycles at physically realizable parameters. We show that complexity in network topology is not necessary for complex behaviors to arise and that nonlinear rheology, in particular the plasma skimming effect, is sufficient to support oscillatory dynamics similar to those observed in vivo.

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less

Managing Complexity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chassin, David P.; Posse, Christian; Malard, Joel M.

2004-08-01

Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today’s most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically-based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This paper explores the state of the art in the use physical analogs for understanding the behavior of some econophysical systems and to deriving stable and robust controlmore » strategies for them. In particular we review and discussion applications of some analytic methods based on the thermodynamic metaphor according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood.« less

Atomic switch networks as complex adaptive systems

NASA Astrophysics Data System (ADS)

Scharnhorst, Kelsey S.; Carbajal, Juan P.; Aguilera, Renato C.; Sandouk, Eric J.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

2018-03-01

Complexity is an increasingly crucial aspect of societal, environmental and biological phenomena. Using a dense unorganized network of synthetic synapses it is shown that a complex adaptive system can be physically created on a microchip built especially for complex problems. These neuro-inspired atomic switch networks (ASNs) are a dynamic system with inherent and distributed memory, recurrent pathways, and up to a billion interacting elements. We demonstrate key parameters describing self-organized behavior such as non-linearity, power law dynamics, and multistate switching regimes. Device dynamics are then investigated using a feedback loop which provides control over current and voltage power-law behavior. Wide ranging prospective applications include understanding and eventually predicting future events that display complex emergent behavior in the critical regime.

Complex and biofluids: From Maxwell to nowadays

NASA Astrophysics Data System (ADS)

Misbah, Chaouqi

2009-11-01

Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

Control of complex physically simulated robot groups

NASA Astrophysics Data System (ADS)

Brogan, David C.

2001-10-01

Actuated systems such as robots take many forms and sizes but each requires solving the difficult task of utilizing available control inputs to accomplish desired system performance. Coordinated groups of robots provide the opportunity to accomplish more complex tasks, to adapt to changing environmental conditions, and to survive individual failures. Similarly, groups of simulated robots, represented as graphical characters, can test the design of experimental scenarios and provide autonomous interactive counterparts for video games. The complexity of writing control algorithms for these groups currently hinders their use. A combination of biologically inspired heuristics, search strategies, and optimization techniques serve to reduce the complexity of controlling these real and simulated characters and to provide computationally feasible solutions.

Dynamical complexity detection in geomagnetic activity indices using wavelet transforms and Tsallis entropy

NASA Astrophysics Data System (ADS)

Balasis, G.; Daglis, I. A.; Papadimitriou, C.; Kalimeri, M.; Anastasiadis, A.; Eftaxias, K.

2008-12-01

Dynamical complexity detection for output time series of complex systems is one of the foremost problems in physics, biology, engineering, and economic sciences. Especially in magnetospheric physics, accurate detection of the dissimilarity between normal and abnormal states (e.g. pre-storm activity and magnetic storms) can vastly improve space weather diagnosis and, consequently, the mitigation of space weather hazards. Herein, we examine the fractal spectral properties of the Dst data using a wavelet analysis technique. We show that distinct changes in associated scaling parameters occur (i.e., transition from anti- persistent to persistent behavior) as an intense magnetic storm approaches. We then analyze Dst time series by introducing the non-extensive Tsallis entropy, Sq, as an appropriate complexity measure. The Tsallis entropy sensitively shows the complexity dissimilarity among different "physiological" (normal) and "pathological" states (intense magnetic storms). The Tsallis entropy implies the emergence of two distinct patterns: (i) a pattern associated with the intense magnetic storms, which is characterized by a higher degree of organization, and (ii) a pattern associated with normal periods, which is characterized by a lower degree of organization.

The Effects Of Physical And Biological Cohesion On Bedforms

NASA Astrophysics Data System (ADS)

Parsons, D. R.; Schindler, R.; Baas, J.; Hope, J. A.; Malarkey, J.; Paterson, D. M.; Peakall, J.; Manning, A. J.; Ye, L.; Aspden, R.; Alan, D.; Bass, S. J.

2014-12-01

Most coastal sediments consist of complex mixtures of cohesionless sands, physically-cohesive clays and extra cellular polymeric substances (EPS) that impart biological cohesion. Yet, our ability to predict bedform dimensions in these substrates is reliant on predictions based exclusively on cohesionless sand. We present findings from the COHBED project - which explicitly examines how bedform dynamics are modified by natural cohesion. Our experimental results show that for ripples, height and length are inversely proportional to initial clay content and bedforms take longer to appear, with no ripples when clay content exceeds 18%. When clay is replaced by EPS the development time and time of first appearance of ripples both increase by two orders of magnitude, with no bedforms above 0.125% EPS. For dunes, height and length are also inversely proportional to initial substrate clay content, resulting in a transition from dunes to ripples normally associated with velocity decreases. Addition of low EPS concentrations into the substrate results in yet smaller bedforms at the same clay contents and at high EPS concentrations, biological cohesion supersedes all electrostatic bonding, and bedform size is no longer related to mud content. The contrast in physical and biological cohesion effects on bedform development result from the disparity between inter-particle electrostatic bonding of clay particles and EPS grain coating and strands that physically link sediments together, which effects winnowing rates as bedforms evolve. These findings have wide ranging implications for bedform predictions in both modern and ancient environments. Coupling of biological and morphological processes not only requires an understanding of how bedform dimensions influence biota and habitat, but also how benthic species can modify bedform dimensions. Consideration of both aspects provides a means in which fluid dynamics, sediment transport and ecosystem energetics can be linked to yield improved predictions of morphological and habitat adjustment.

Network biology discovers pathogen contact points in host protein-protein interactomes.

PubMed

Ahmed, Hadia; Howton, T C; Sun, Yali; Weinberger, Natascha; Belkhadir, Youssef; Mukhtar, M Shahid

2018-06-13

In all organisms, major biological processes are controlled by complex protein-protein interactions networks (interactomes), yet their structural complexity presents major analytical challenges. Here, we integrate a compendium of over 4300 phenotypes with Arabidopsis interactome (AI-1 MAIN ). We show that nodes with high connectivity and betweenness are enriched and depleted in conditional and essential phenotypes, respectively. Such nodes are located in the innermost layers of AI-1 MAIN and are preferential targets of pathogen effectors. We extend these network-centric analyses to Cell Surface Interactome (CSI LRR ) and predict its 35 most influential nodes. To determine their biological relevance, we show that these proteins physically interact with pathogen effectors and modulate plant immunity. Overall, our findings contrast with centrality-lethality rule, discover fast information spreading nodes, and highlight the structural properties of pathogen targets in two different interactomes. Finally, this theoretical framework could possibly be applicable to other inter-species interactomes to reveal pathogen contact points.

New strategy for protein interactions and application to structure-based drug design

NASA Astrophysics Data System (ADS)

Zou, Xiaoqin

One of the greatest challenges in computational biophysics is to predict interactions between biological molecules, which play critical roles in biological processes and rational design of therapeutic drugs. Biomolecular interactions involve delicate interplay between multiple interactions, including electrostatic interactions, van der Waals interactions, solvent effect, and conformational entropic effect. Accurate determination of these complex and subtle interactions is challenging. Moreover, a biological molecule such as a protein usually consists of thousands of atoms, and thus occupies a huge conformational space. The large degrees of freedom pose further challenges for accurate prediction of biomolecular interactions. Here, I will present our development of physics-based theory and computational modeling on protein interactions with other molecules. The major strategy is to extract microscopic energetics from the information embedded in the experimentally-determined structures of protein complexes. I will also present applications of the methods to structure-based therapeutic design. Supported by NSF CAREER Award DBI-0953839, NIH R01GM109980, and the American Heart Association (Midwest Affiliate) [13GRNT16990076].

Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

PubMed Central

Wang, Yuefeng; Fisher, John C.; Mathew, Rose; Ou, Li; Otieno, Steve; Sublett, Jack; Xiao, Limin; Chen, Jianhan; Roussel, Martine F.; Kriwacki, Richard W.

2011-01-01

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. PMID:21358637

On the spatial heterogeneity of net ecosystem productivity in complex landscapes

Treesearch

Ryan E. Emanuel; Diego A. Riveros-Iregui; Brian L. McGlynn; Howard E. Epstein

2011-01-01

Micrometeorological flux towers provide spatially integrated estimates of net ecosystem production (NEP) of carbon over areas ranging from several hectares to several square kilometers, but they do so at the expense of spatially explicit information within the footprint of the tower. This finer-scale information is crucial for understanding how physical and biological...

A benchmark-multi-disciplinary study of the interaction between the Chesapeake Bay and adjacent waters of the Virginian Sea

NASA Technical Reports Server (NTRS)

Hargis, W. J., Jr.

1981-01-01

The social and economic importance of estuaries are discussed. Major focus is on the Chesapeake Bay and its interaction with the adjacent waters of the Virginia Sea. Associated multiple use development and management problems as well as their internal physical, geological, chemical, and biological complexities are described.

Strand IV Environmental and Community Health, Ecology and Epidemiology of Health, Grades 10, 11, and 12.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of Secondary Curriculum Development.

A frame of reference concerning health implications, based on the interaction of numerous factors in the physical, social, and biological environments, is provided in this prototype curriculum for grades 10-12. Development of sound techniques in problem solving is encouraged, resulting from the need to understand the nature and complexities of…

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuemann, J.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less

Prediction of lung cells oncogenic transformation for induced radon progeny alpha particles using sugarscape cellular automata.

PubMed

Baradaran, Samaneh; Maleknasr, Niaz; Setayeshi, Saeed; Akbari, Mohammad Esmaeil

2014-01-01

Alpha particle irradiation from radon progeny is one of the major natural sources of effective dose in the public population. Oncogenic transformation is a biological effectiveness of radon progeny alpha particle hits. The biological effects which has caused by exposure to radon, were the main result of a complex series of physical, chemical, biological and physiological interactions. The cellular and molecular mechanisms for radon-induced carcinogenesis have not been clear yet. Various biological models, including cultured cells and animals, have been found useful for studying the carcinogenesis effects of radon progeny alpha particles. In this paper, sugars cape cellular automata have been presented for computational study of complex biological effect of radon progeny alpha particles in lung bronchial airways. The model has included mechanism of DNA damage, which has been induced alpha particles hits, and then formation of transformation in the lung cells. Biomarkers were an objective measure or evaluation of normal or abnormal biological processes. In the model, the metabolism rate of infected cell has been induced alpha particles traversals, as a biomarker, has been followed to reach oncogenic transformation. The model results have successfully validated in comparison with "in vitro oncogenic transformation data" for C3H 10T1/2 cells. This model has provided an opportunity to study the cellular and molecular changes, at the various stages in radiation carcinogenesis, involving human cells. It has become well known that simulation could be used to investigate complex biomedical systems, in situations where traditional methodologies were difficult or too costly to employ.

Animal models and conserved processes

PubMed Central

2012-01-01

Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible. PMID:22963674

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach.

PubMed

van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A

2015-11-07

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

Physical characteristics of the gonadotropin receptor-hormone complexes formed in vivo and in vitro.

PubMed Central

Dufau, M L; Podesta, E J; Catt, K J

1975-01-01

The physical properties of detergent-solubilized gonadotropin receptor-hormone complexes, determined by density gradient centrifugation and gel filtration, were compared after in vivo and in vitro labeling of specific ovarian binding sites with radioiodinated human chorionic gonadotropin (hCG). Following intravenous administration of biologically active 125I-labeled hCG, up to 50% of the gonadotropin tracer was bound to the luteinized ovaries of immature female rats treated with pregnant mare serum/human chorionic gonadotropin. Comparable binding of 125I-labeled hCG was observed after equilibration of ovarian particles with the labeled hormone in vitro. The sedimentation properties of the solubilized receptor-hormone complexes formed in vivo were identical with those derived for the corresponding complexes formed in vitro and extracted with Triton X-100 and Lubrol PX, with sedimentation constants of 8.8 S for the Triton-solubilized complex and 7.0 S for the complex extracted with Lubrol PX. During analytical gel filtration of the Triton-solubilized receptor-hormone complex on Sepharose 6B in 0.1% Triton X-100, the partition coefficient (Kav) of the "in vivo" complex (0.32) was not significantly different from that of the complex formed in vitro (0.29). Gel filtration of the Lubrol-solubilized ovarian particles on Sepharose 6B in 0.5% Lubrol PX gave Kav values for the "in vivo" and "in vitro" labeled complexes of 0.36 and 0.32, respectively. These findings demonstrate that the physical properties of size and shape which determine the partition coefficient and sedimentation characteristics of detergent-solubilized gonadotropin receptor-hormone complexes formed in vitro are not distinguishable from those of the complexes extracted after specific interaction of the ovarian gonadotropin receptors with radioiodinated hCG in vivo. PMID:165502

The science of complexity and the role of mathematics

NASA Astrophysics Data System (ADS)

Bountis, T.; Johnson, J.; Provata, A.; Tsironis, G.

2016-09-01

In the middle of the second decade of the 21st century, Complexity Science has reached a turning point. Its rapid advancement over the last 30 years has led to remarkable new concepts, methods and techniques, whose applications to complex systems of the physical, biological and social sciences has produced a great number of exciting results. The approach has so far depended almost exclusively on the solution of a wide variety of mathematical models by sophisticated numerical techniques and extensive simulations that have inspired a new generation of researchers interested in complex systems. Still, the impact of Complexity beyond the natural sciences, its applications to Medicine, Technology, Economics, Society and Policy are only now beginning to be explored. Furthermore, its basic principles and methods have so far remained within the realm of high level research institutions, out of reach of society's urgent need for practical applications. To address these issues, evaluate the current situation and bring Complexity Science closer to university students, a series of Ph.D. Schools on Mathematical Modeling of Complex Systems was launched, starting in July 2011 at the University of Patras, Greece (see http://www.math.upatras.gr/˜phdsch11). These Schools lasted two weeks each and included, beyond introductory lectures, a conference component of 2-3 days where students were exposed to recent results mainly presented by young researchers. The Ph.D. Schools continued successfully, the 2nd one taking place at Pescara, Italy (2012), (see http://www.nodycosy.unich.it), the 3d one at Heraklion, Crete, Greece (2013) (see http://nlsconf2013.physics.uoc.gr) and the 4th one in Athens, Greece (2014) (see http://nlsconf2014.physics.uoc.gr) (2014). This Special Theme volume contains the proceedings of the 5th Ph.D. School-Conference of this series held at the University of Patras, Greece, 20 30 July, 2015 (see http://www.math.upatras.gr/˜phdsch15) and includes many of the introductory lectures and research talks presented at this event. The primary concern of all those that participated in these events was to emphasize the role of mathematics, modeling and numerical simulation, which are indispensable for understanding what we call complex behavior of physical, biological, technological and socio - economical systems. In the discussions that took place, a great number of participants expressed the need to formulate a unifying theory of complex systems based on the main conclusions that have been reached so far in the science of Complexity. As Guest Editors of this volume, we also feel that it is important to reach some fundamental conclusions concerning common phenomena, theories and methodologies that arise in Complexity. We should all work to explore common rules and approaches, particularly in view of the remarkable challenges that face us all regarding complex social problems that threaten present day society and civilization as we know them.

A process-based hierarchical framework for monitoring glaciated alpine headwaters

USGS Publications Warehouse

Weekes, Anne A.; Torgersen, Christian E.; Montgomery, David R.; Woodward, Andrea; Bolton, Susan M.

2012-01-01

Recent studies have demonstrated the geomorphic complexity and wide range of hydrologic regimes found in alpine headwater channels that provide complex habitats for aquatic taxa. These geohydrologic elements are fundamental to better understand patterns in species assemblages and indicator taxa and are necessary to aquatic monitoring protocols that aim to track changes in physical conditions. Complex physical variables shape many biological and ecological traits, including life history strategies, but these mechanisms can only be understood if critical physical variables are adequately represented within the sampling framework. To better align sampling design protocols with current geohydrologic knowledge, we present a conceptual framework that incorporates regional-scale conditions, basin-scale longitudinal profiles, valley-scale glacial macroform structure, valley segment-scale (i.e., colluvial, alluvial, and bedrock), and reach-scale channel types. At the valley segment- and reach-scales, these hierarchical levels are associated with differences in streamflow and sediment regime, water source contribution and water temperature. Examples of linked physical-ecological hypotheses placed in a landscape context and a case study using the proposed framework are presented to demonstrate the usefulness of this approach for monitoring complex temporal and spatial patterns and processes in glaciated basins. This approach is meant to aid in comparisons between mountain regions on a global scale and to improve management of potentially endangered alpine species affected by climate change and other stressors.

An initial physical mechanism in the treatment of neurologic disorders with externally applied pico Tesla magnetic fields.

PubMed

Jacobson, J I; Yamanashi, W S

1995-04-01

The recent clinical studies describing the treatment of some neurological disorders with an externally applied pico Tesla (10(-12) Tesla, or 10(-8) gauss) magnetic field are considered from a physical view point. An equation relating the intrinsic (or rest) energy of a charged particle of mass m with its energy of interaction in an externally applied magnetic field B is presented. The equation represents an initial basic physical interaction as a part of a more complex biological mechanism to explain the therapeutic effects of externally applied magnetic fields in these and other neurologic disorders.

A physical mechanism in the treatment of neurologic disorders with externally applied pico Tesla magnetic fields.

PubMed

Jacobson, J I; Yamanashi, W S

1995-06-01

The clinical studies describing the treatment of some neurological disorders with an externally applied pico Tesla (10R Tesla, or 10(-8) gauss) magnetic field are considered from a physical view point. An equation relating the intrinsic or "rest" energy of a charged particle of mass with its energy of interaction in an externally applied magnetic field B is presented. The equation is proposed to represent an initial basic physical interaction as a part of a more complex biological mechanism to explain the therapeutic effects of externally applied magnetic fields in these and other neurologic disorders.

From physical to biological individuation.

PubMed

Miquel, Paul-Antoine; Hwang, Su-Young

2016-10-01

In this paper, we insist on stressing the epistemic and metaphysical difference between individual and individuation, a distinction originally developed by Gilbert Simondon. Individuation occurs in complex physical systems by the coupling (R 1 ) between the system and its outside conditions. As such the system is not well defined by its sole constituents. Let's characterize (R 2 ) as follows: the system is not entirely defined by its structure at a given time because this structure will change and global emergent properties will appear, as in the paradigmatic example of phase transition. Thus physical individuation is defined both by the coupling of a physical system with its environment (R 1 ) and by its diachronic dynamics taking place (R 2 ). We interpret biological individuation as a second order one, i.e. as a recursive procedure through which physical individuation is also acting on "its own theatre". We represent this procedure like a mapping through which (R 1 R 2 ) are applied to themselves, so that: R N  = (R 1 R 2 ) N . We highlight the relation between this assumption and the concept of extended criticality developed by Bailly, Longo and Montévil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Neuromorphic neural interfaces: from neurophysiological inspiration to biohybrid coupling with nervous systems

NASA Astrophysics Data System (ADS)

Broccard, Frédéric D.; Joshi, Siddharth; Wang, Jun; Cauwenberghs, Gert

2017-08-01

Objective. Computation in nervous systems operates with different computational primitives, and on different hardware, than traditional digital computation and is thus subjected to different constraints from its digital counterpart regarding the use of physical resources such as time, space and energy. In an effort to better understand neural computation on a physical medium with similar spatiotemporal and energetic constraints, the field of neuromorphic engineering aims to design and implement electronic systems that emulate in very large-scale integration (VLSI) hardware the organization and functions of neural systems at multiple levels of biological organization, from individual neurons up to large circuits and networks. Mixed analog/digital neuromorphic VLSI systems are compact, consume little power and operate in real time independently of the size and complexity of the model. Approach. This article highlights the current efforts to interface neuromorphic systems with neural systems at multiple levels of biological organization, from the synaptic to the system level, and discusses the prospects for future biohybrid systems with neuromorphic circuits of greater complexity. Main results. Single silicon neurons have been interfaced successfully with invertebrate and vertebrate neural networks. This approach allowed the investigation of neural properties that are inaccessible with traditional techniques while providing a realistic biological context not achievable with traditional numerical modeling methods. At the network level, populations of neurons are envisioned to communicate bidirectionally with neuromorphic processors of hundreds or thousands of silicon neurons. Recent work on brain-machine interfaces suggests that this is feasible with current neuromorphic technology. Significance. Biohybrid interfaces between biological neurons and VLSI neuromorphic systems of varying complexity have started to emerge in the literature. Primarily intended as a computational tool for investigating fundamental questions related to neural dynamics, the sophistication of current neuromorphic systems now allows direct interfaces with large neuronal networks and circuits, resulting in potentially interesting clinical applications for neuroengineering systems, neuroprosthetics and neurorehabilitation.

RNA Helicases at work: binding and rearranging

PubMed Central

Jankowsky, Eckhard

2010-01-01

RNA helicases are ubiquitous, highly conserved enzymes that participate in nearly all aspects of RNA metabolism. These proteins bind or remodel RNA or RNA–protein complexes in an ATP-dependent fashion. How RNA helicases physically perform their cellular tasks has been a longstanding question, but in recent years, intriguing models have started to link structure, mechanism and biological function for some RNA helicases. This review outlines our current view on major structural and mechanistic themes of RNA helicase function, and on emerging physical models for cellular roles of these enzymes. PMID:20813532

An Investigation of Methods to Measure and Predict Biological and Physical Effects of Commercial Navigation Traffic: Workshop II Held in St. Louis, Missouri on 17-18 April 1990

DTIC Science & Technology

1991-04-01

task of measurinig these forces in the natural environment and the increasing need to predict how these forces will ultimately affect the environment...near and beneath a towboat are complex and three-dimensional. These flow conditions are affected by physical conditions such as the shape and size of...a highly quantitative and fruitful line of pure and applied stud- ies of aquatic animal life histories (e.g., Russell Hunter (1953), Fremling (1960

Network dynamics and systems biology

NASA Astrophysics Data System (ADS)

Norrell, Johannes A.

The physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior. In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects---an asymmetry between on and off states, and a decaying memory of events in each element's inputs---that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors. Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the transition point, called critical, exhibit many of the features of regulatory networks, and recent studies suggest that some specific regulatory networks are indeed near-critical. We ask whether certain statistical measures of the ensemble behavior of large continuous networks are reproduced by Boolean models. We find that, in spite of the lack of correspondence between attractors observed in smaller systems, the statistical characterization given by the continuous and Boolean models show close agreement, and the transition between order and disorder known in Boolean systems can occur in continuous systems as well. One effect that is not present in Boolean systems, the failure of information to propagate down chains of elements of arbitrary length, is present in a class of continuous networks. In these systems, a modified Boolean theory that takes into account the collective effect of propagation failure on chains throughout the network gives a good description of the observed behavior. We find that propagation failure pushes the system toward greater order, resulting in a partial or complete suppression of the disordered phase. Finally, we explore a dynamical process of direct biological relevance: asymmetric cell division in A. thaliana. The long term goal is to develop a model for the process that accurately accounts for both wild type and mutant behavior. To contribute to this endeavor, we use confocal microscopy to image roots in a SHORT-ROOT inducible mutant. We compute correlation functions between the locations of asymmetrically divided cells, and we construct stochastic models based on a few simple assumptions that accurately predict the non-zero correlations. Our result shows that intracellular processes alone cannot be responsible for the observed divisions, and that an intercell signaling mechanism could account for the measured correlations.

The Capabilities of Chaos and Complexity

PubMed Central

Abel, David L.

2009-01-01

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization? PMID:19333445

Assessing Vermont's stream health and biological integrity using artificial neural networks and Bayesian methods

NASA Astrophysics Data System (ADS)

Rizzo, D. M.; Fytilis, N.; Stevens, L.

2012-12-01

Environmental managers are increasingly required to monitor and forecast long-term effects and vulnerability of biophysical systems to human-generated stresses. Ideally, a study involving both physical and biological assessments conducted concurrently (in space and time) could provide a better understanding of the mechanisms and complex relationships. However, costs and resources associated with monitoring the complex linkages between the physical, geomorphic and habitat conditions and the biological integrity of stream reaches are prohibitive. Researchers have used classification techniques to place individual streams and rivers into a broader spatial context (hydrologic or health condition). Such efforts require environmental managers to gather multiple forms of information - quantitative, qualitative and subjective. We research and develop a novel classification tool that combines self-organizing maps with a Naïve Bayesian classifier to direct resources to stream reaches most in need. The Vermont Agency of Natural Resources has developed and adopted protocols for physical stream geomorphic and habitat assessments throughout the state of Vermont. Separate from these assessments, the Vermont Department of Environmental Conservation monitors the biological communities and the water quality in streams. Our initial hypothesis is that the geomorphic reach assessments and water quality data may be leveraged to reduce error and uncertainty associated with predictions of biological integrity and stream health. We test our hypothesis using over 2500 Vermont stream reaches (~1371 stream miles) assessed by the two agencies. In the development of this work, we combine a Naïve Bayesian classifier with a modified Kohonen Self-Organizing Map (SOM). The SOM is an unsupervised artificial neural network that autonomously analyzes inherent dataset properties using input data only. It is typically used to cluster data into similar categories when a priori classes do not exist. The incorporation of a Bayesian classifier allows one to explicitly incorporate existing knowledge and expert opinion into the data analysis. Since classification plays a leading role in the future development of data-enabled science and engineering, such a computational tool is applicable to a variety of proactive adaptive watershed management applications.

PREFACE: Statistical Physics of Complex Fluids

NASA Astrophysics Data System (ADS)

Golestanian, R.; Khajehpour, M. R. H.; Kolahchi, M. R.; Rouhani, S.

2005-04-01

The field of complex fluids is a rapidly developing, highly interdisciplinary field that brings together people from a plethora of backgrounds such as mechanical engineering, chemical engineering, materials science, applied mathematics, physics, chemistry and biology. In this melting pot of science, the traditional boundaries of various scientific disciplines have been set aside. It is this very property of the field that has guaranteed its richness and prosperity since the final decade of the 20th century and into the 21st. The C3 Commission of the International Union of Pure and Applied Physics (IUPAP), which is the commission for statistical physics that organizes the international STATPHYS conferences, encourages various, more focused, satellite meetings to complement the main event. For the STATPHYS22 conference in Bangalore (July 2004), Iran was recognized by the STATPHYS22 organizers as suitable to host such a satellite meeting and the Institute for Advanced Studies in Basic Sciences (IASBS) was chosen to be the site of this meeting. It was decided to organize a meeting in the field of complex fluids, which is a fairly developed field in Iran. This international meeting, and an accompanying summer school, were intended to boost international connections for both the research groups working in Iran, and several other groups working in the Middle East, South Asia and North Africa. The meeting, entitled `Statistical Physics of Complex Fluids' was held at the Institute for Advanced Studies in Basic Sciences (IASBS) in Zanjan, Iran, from 27 June to 1 July 2004. The main topics discussed at the meeting included: biological statistical physics, wetting and microfluidics, transport in complex media, soft and granular matter, and rheology of complex fluids. At this meeting, 22 invited lectures by eminent scientists were attended by 107 participants from different countries. The poster session consisted of 45 presentations which, in addition to the main topics of the meeting, covered some of the various areas in statistical physics currently active in Iran. About half of the participants came from countries other than Iran, with a relatively broad geographic distribution. The meeting benefited greatly from the excellent administrative assistance of the conference secretary Ms Ashraf Moosavi and the IASBS staff. We are grateful to Professor Yousef Sobouti, the Director of IASBS, and Professor Reza Mansouri, the Head of the Physical Society of Iran, for their support. We also thank the organizers of STATPHYS22, Professor Rahul Pandit and his colleagues, for their suggestions and support. The conference was supported by donations from the Center for International Research and Collaboration (ISMO) and the Institute for Research and Planning in Higher Education (IRPHE) of the Iranian Ministry of Science, Research and Technology, the Islamic Development Bank, the Abdus Salam International Centre for Theoretical Physics (ICTP), the Tehran Cluster Office of the United Nations Educational, Scientific and Cultural Organization (UNESCO), the Research and Development Directorate of the National Iranian Oil Company, the Physical Society of Iran, the Iranian Meteorological Organization, and the Zanjan City Water and Waste Water Company. Finally, we would like to express our gratitude to Institute of Physics Publishing, and in particular to Professor Alexei Kornyshev and Dr Richard Palmer for suggesting publishing the proceedings of the meeting and carrying through the editorial processes with the utmost efficiency. Participants

Protein-protein interaction networks (PPI) and complex diseases

PubMed Central

Safari-Alighiarloo, Nahid; Taghizadeh, Mohammad; Rezaei-Tavirani, Mostafa; Goliaei, Bahram

2014-01-01

The physical interaction of proteins which lead to compiling them into large densely connected networks is a noticeable subject to investigation. Protein interaction networks are useful because of making basic scientific abstraction and improving biological and biomedical applications. Based on principle roles of proteins in biological function, their interactions determine molecular and cellular mechanisms, which control healthy and diseased states in organisms. Therefore, such networks facilitate the understanding of pathogenic (and physiologic) mechanisms that trigger the onset and progression of diseases. Consequently, this knowledge can be translated into effective diagnostic and therapeutic strategies. Furthermore, the results of several studies have proved that the structure and dynamics of protein networks are disturbed in complex diseases such as cancer and autoimmune disorders. Based on such relationship, a novel paradigm is suggested in order to confirm that the protein interaction networks can be the target of therapy for treatment of complex multi-genic diseases rather than individual molecules with disrespect the network. PMID:25436094

3D bioprinting of tissues and organs.

PubMed

Murphy, Sean V; Atala, Anthony

2014-08-01

Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology.

Evolution of speech and evolution of language.

PubMed

de Boer, Bart

2017-02-01

Speech is the physical signal used to convey spoken language. Because of its physical nature, speech is both easier to compare with other species' behaviors and easier to study in the fossil record than other aspects of language. Here I argue that convergent fossil evidence indicates adaptations for complex vocalizations at least as early as the common ancestor of Neanderthals and modern humans. Furthermore, I argue that it is unlikely that language evolved separately from speech, but rather that gesture, speech, and song coevolved to provide both a multimodal communication system and a musical system. Moreover, coevolution must also have played a role by allowing both cognitive and anatomical adaptations to language and speech to evolve in parallel. Although such a coevolutionary scenario is complex, it is entirely plausible from a biological point of view.

Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

NASA Astrophysics Data System (ADS)

Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

2018-03-01

Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

Your actions in my cerebellum: subclinical deficits in action observation in patients with unilateral chronic cerebellar stroke.

PubMed

Cattaneo, Luigi; Fasanelli, Monica; Andreatta, Olaf; Bonifati, Domenico Marco; Barchiesi, Guido; Caruana, Fausto

2012-03-01

Empirical evidence indicates that cognitive consequences of cerebellar lesions tend to be mild and less important than the symptoms due to lesions to cerebral areas. By contrast, imaging studies consistently report strong cerebellar activity during tasks of action observation and action understanding. This has been interpreted as part of the automatic motor simulation process that takes place in the context of action observation. The function of the cerebellum as a sequencer during executed movements makes it a good candidate, within the framework of embodied cognition, for a pivotal role in understanding the timing of action sequences. Here, we investigated a cohort of eight patients with chronic, first-ever, isolated, ischemic lesions of the cerebellum. The experimental task consisted in identifying a plausible sequence of pictures from a randomly ordered group of still frames extracted from (a) a complex action performed by a human actor ("biological action" test) or (b) a complex physical event occurring to an inanimate object ("folk physics" test). A group of 16 healthy participants was used as control. The main result showed that cerebellar patients performed significantly worse than controls in both sequencing tasks, but performed much worse in the "biological action" test than in the "folk physics" test. The dissociation described here suggests that observed sequences of simple motor acts seem to be represented differentially from other sequences in the cerebellum.

"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

PubMed

Sato, Naoki

2018-05-01

"What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life. Another, prevalent idea emphasizes that life resides in the whole system of an organism, but not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. These two views are both materialistic and mechanistic, and act as driving forces of modern biology. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. A key notion to reconcile this conflict is that subjects of biological studies are given before we start to study them. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecosystem health in mineralized terrane; data from podiform chromite (Chinese Camp mining district, California), quartz alunite (Castle Peak and Masonic mining districts, Nevada/California), and Mo/Cu porphyry (Battle Mountain mining district, Nevada) deposits

USGS Publications Warehouse

Blecker, Steve W.; Stillings, Lisa L.; Amacher, Michael C.; Ippolito, James A.; DeCrappeo, Nicole M.

2010-01-01

The myriad definitions of soil/ecosystem quality or health are often driven by ecosystem and management concerns, and they typically focus on the ability of the soil to provide functions relating to biological productivity and/or environmental quality. A variety of attempts have been made to create indices that quantify the complexities of soil quality and provide a means of evaluating the impact of various natural and anthropogenic disturbances. Though not without their limitations, indices can improve our understanding of the controls behind ecosystem processes and allow for the distillation of information to help link scientific and management communities. In terrestrial systems, indices were initially developed and modified for agroecosystems; however, the number of studies implementing such indices in nonagricultural systems is growing. Soil quality indices (SQIs) are typically composed of biological (and sometimes physical and chemical) parameters that attempt to reduce the complexity of a system into a metric of a soil’s ability to carry out one or more functions.The indicators utilized in SQIs can be as varied as the studies themselves, reflecting the complexity of the soil and ecosystems in which they function. Regardless, effective soil quality indicators should correlate well with soil or ecosystem processes, integrate those properties and processes, and be relevant to management practices. Commonly applied biological indicators include measures associated with soil microbial activity or function (for example, carbon and nitrogen mineralization, respiration, microbial biomass, enzyme activity. Cost, accessibility, ease of interpretation, and presence of existing data often dictate indicator selection given the number of available measures. We employed a large number of soil biological, chemical, and physical measures, along with measures of vegetation cover, density, and productivity, in order to test the utility and sensitivity of these measures within various mineralized terranes. We were also interested in examining these relations in the context of determining appropriate reference conditions with which to compare reclamation efforts.The purpose of this report is to present the data used to develop indices of soil and ecosystem quality associated with mineralized terranes (areas enriched in metal-bearing minerals), specifically podiform chromite, quartz alunite, and Mo/Cu porphyry systems. Within each of these mineralized terranes, a nearby unmineralized counterpart was chosen for comparison. The data consist of soil biological, chemical, and physical parameters, along with vegetation measurements for each of the sites described below. Synthesis of these data and index development will be the subject of future publications.

Coupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries

USGS Publications Warehouse

Koseff, Jeffrey R.; Holen, Jacqueline K.; Monismith, Stephen G.; Cloern, James E.

1993-01-01

Coastal ocean waters tend to have very different patterns of phytoplankton biomass variability from the open ocean, and the connections between physical variability and phytoplankton bloom dynamics are less well established for these shallow systems. Predictions of biological responses to physical variability in these environments is inherently difficult because the recurrent seasonal patterns of mixing are complicated by aperiodic fluctuations in river discharge and the high-frequency components of tidal variability. We might expect, then, less predictable and more complex bloom dynamics in these shallow coastal systems compared with the open ocean. Given this complex and dynamic physical environment, can we develop a quantitative framework to define the physical regimes necessary for bloom inception, and can we identify the important mechanisms of physical-biological coupling that lead to the initiation and termination of blooms in estuaries and shallow coastal waters? Numerical modeling provides one approach to address these questions. Here we present results of simulation experiments with a refined version of Cloern's (1991) model in which mixing processes are treated more realistically to reflect the dynamic nature of turbulence generation in estuaries. We investigated several simple models for the turbulent mixing coefficient. We found that the addition of diurnal tidal variation to Cloern's model greatly reduces biomass growth indicating that variations of mixing on the time scale of hours are crucial. Furthermore, we found that for conditions representative of South San Francisco Bay, numerical simulations only allowed for bloom development when the water column was stratified and when minimal mixing was prescribed in the upper layer. Stratification, however, itself is not sufficient to ensure that a bloom will develop: minimal wind stirring is a further prerequisite to bloom development in shallow turbid estuaries with abundant populations of benthic suspension feeders.

Theoretical description of protein field effects on electronic excitations of biological chromophores.

PubMed

Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

2017-01-11

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

Theoretical description of protein field effects on electronic excitations of biological chromophores

NASA Astrophysics Data System (ADS)

Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

2017-01-01

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

Complexation of C60 fullerene with aromatic drugs.

PubMed

Evstigneev, Maxim P; Buchelnikov, Anatoly S; Voronin, Dmitry P; Rubin, Yuriy V; Belous, Leonid F; Prylutskyy, Yuriy I; Ritter, Uwe

2013-02-25

The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Charting environmental pollution. [by noise measurements

NASA Technical Reports Server (NTRS)

Halpert, E.; Bizo, F.; Karacsonyi, Z.

1974-01-01

It is found that areas affected by different noxious agents are within the limits traced for high noise level areas; consequently, it is suggested that high noise pressure levels should be used as the primary indication of environmental pollution. A complex methodology is reported for charting environmental pollution due to physical, chemical and biological noxious agents on the scale of an industrial district.

Biological Inspiration for Agile Autonomous Air Vehicles

DTIC Science & Technology

2007-11-01

rhythmically contract the thorax; the hind wings have become specialized as small body rotation sensors (halteres). Butterflies and moths have two pairs of...orthogonal pairs of power muscles that produce alternating dorso-ventral and longitudinal flexure of the thorax from rhythmic contractions similar to...other physical sciences lend themselves to somewhat reductionist approaches for both analysis and synthesis. Complex engineered systems are built from

The origin of neutron biological effectiveness as a function of energy.

PubMed

Baiocco, G; Barbieri, S; Babini, G; Morini, J; Alloni, D; Friedland, W; Kundrát, P; Schmitt, E; Puchalska, M; Sihver, L; Ottolenghi, A

2016-09-22

The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data.

The origin of neutron biological effectiveness as a function of energy

NASA Astrophysics Data System (ADS)

Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

2016-09-01

The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data.

Physics must join with biology in better assessing risk from low-dose irradiation.

PubMed

Feinendegen, L E; Neumann, R D

2005-01-01

This review summarises the complex response of mammalian cells and tissues to low doses of ionising radiation. This thesis encompasses induction of DNA damage, and adaptive protection against both renewed damage and against propagation of damage from the basic level of biological organisation to the clinical expression of detriment. The induction of DNA damage at low radiation doses apparently is proportional to absorbed dose at the physical/chemical level. However, any propagation of such damage to higher levels of biological organisation inherently follows a sigmoid function. Moreover, low-dose-induced inhibition of damage propagation is not linear, but instead follows a dose-effect function typical for adaptive protection, after an initial rapid rise it disappears at doses higher than approximately 0.1-0.2 Gy to cells. The particular biological response duality at low radiation doses precludes the validity of the linear-no-threshold hypothesis in the attempt to relate absorbed dose to cancer. In fact, theory and observation support not only a lower cancer incidence than expected from the linear-no-threshold hypothesis, but also a reduction of spontaneously occurring cancer, a hormetic response, in the healthy individual.

The origin of neutron biological effectiveness as a function of energy

PubMed Central

Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

2016-01-01

The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. PMID:27654349

Determinism, chaos, self-organization and entropy.

PubMed

Pontes, José

2016-01-01

We discuss two changes of paradigms that occurred in science along the XXth century: the end of the mechanist determinism, and the end of the apparent incompatibility between biology, where emergence of order is law, and physics, postulating a progressive loss of order in natural systems. We recognize today that three mechanisms play a major role in the building of order: the nonlinear nature of most evolution laws, along with distance to equilibrium, and with the new paradigm, that emerged in the last forty years, as we recognize that networks present collective order properties not found in the individual nodes. We also address the result presented by Blumenfeld (L.A. Blumenfeld, Problems of Biological Physics, Springer, Berlin, 1981) showing that entropy decreases resulting from building one of the most complex biological structures, the human being, are small and may be trivially compensated for compliance with thermodynamics. Life is made at the expense of very low thermodynamic cost, so thermodynamics does not pose major restrictions to the emergence of life. Besides, entropy does not capture our idea of order in biological systems. The above questions show that science is not free of confl icts and backlashes, often resulting from excessive extrapolations.

Impact of negative cognitions about body image on inflammatory status in relation to health.

PubMed

Černelič-Bizjak, Maša; Jenko-Pražnikar, Zala

2014-01-01

Evidence suggests that body dissatisfaction may relate to biological processes and that negative cognitions can influence physical health through the complex pathways linking psychological and biological factors. The present study investigates the relationships between body image satisfaction, inflammation (cytokine levels), aerobic fitness level and obesity in 96 middle-aged men and women (48 normal and 48 overweight). All participants underwent measurements of body satisfaction, body composition, serological measurements of inflammation and aerobic capabilities assessment. Body image dissatisfaction uniquely predicted inflammation biomarkers, C-reactive protein and tumour necrosis factor-α, even when controlled for obesity indicators. Thus, body image dissatisfaction is strongly linked to inflammation processes and may promote the increase in cytokines, representing a relative metabolic risk, independent of most traditional risk factors, such as gender, body mass index and intra-abdominal (waist to hip ratio) adiposity. Results highlight the fact that person's negative cognitions need to be considered in psychologically based interventions and strategies in treatment of obesity, including strategies for health promotion. Results contribute to the knowledge base of the complex pathways in the association between psychological factors and physical illness and some important attempts were made to explain the psychological pathways linking cognitions with inflammation.

Information processing in bacteria: memory, computation, and statistical physics: a key issues review

NASA Astrophysics Data System (ADS)

Lan, Ganhui; Tu, Yuhai

2016-05-01

Living systems have to constantly sense their external environment and adjust their internal state in order to survive and reproduce. Biological systems, from as complex as the brain to a single E. coli cell, have to process these data in order to make appropriate decisions. How do biological systems sense external signals? How do they process the information? How do they respond to signals? Through years of intense study by biologists, many key molecular players and their interactions have been identified in different biological machineries that carry out these signaling functions. However, an integrated, quantitative understanding of the whole system is still lacking for most cellular signaling pathways, not to say the more complicated neural circuits. To study signaling processes in biology, the key thing to measure is the input-output relationship. The input is the signal itself, such as chemical concentration, external temperature, light (intensity and frequency), and more complex signals such as the face of a cat. The output can be protein conformational changes and covalent modifications (phosphorylation, methylation, etc), gene expression, cell growth and motility, as well as more complex output such as neuron firing patterns and behaviors of higher animals. Due to the inherent noise in biological systems, the measured input-output dependence is often noisy. These noisy data can be analysed by using powerful tools and concepts from information theory such as mutual information, channel capacity, and the maximum entropy hypothesis. This information theory approach has been successfully used to reveal the underlying correlations between key components of biological networks, to set bounds for network performance, and to understand possible network architecture in generating observed correlations. Although the information theory approach provides a general tool in analysing noisy biological data and may be used to suggest possible network architectures in preserving information, it does not reveal the underlying mechanism that leads to the observed input-output relationship, nor does it tell us much about which information is important for the organism and how biological systems use information to carry out specific functions. To do that, we need to develop models of the biological machineries, e.g. biochemical networks and neural networks, to understand the dynamics of biological information processes. This is a much more difficult task. It requires deep knowledge of the underlying biological network—the main players (nodes) and their interactions (links)—in sufficient detail to build a model with predictive power, as well as quantitative input-output measurements of the system under different perturbations (both genetic variations and different external conditions) to test the model predictions to guide further development of the model. Due to the recent growth of biological knowledge thanks in part to high throughput methods (sequencing, gene expression microarray, etc) and development of quantitative in vivo techniques such as various florescence technology, these requirements are starting to be realized in different biological systems. The possible close interaction between quantitative experimentation and theoretical modeling has made systems biology an attractive field for physicists interested in quantitative biology. In this review, we describe some of the recent work in developing a quantitative predictive model of bacterial chemotaxis, which can be considered as the hydrogen atom of systems biology. Using statistical physics approaches, such as the Ising model and Langevin equation, we study how bacteria, such as E. coli, sense and amplify external signals, how they keep a working memory of the stimuli, and how they use these data to compute the chemical gradient. In particular, we will describe how E. coli cells avoid cross-talk in a heterogeneous receptor cluster to keep a ligand-specific memory. We will also study the thermodynamic costs of adaptation for cells to maintain an accurate memory. The statistical physics based approach described here should be useful in understanding design principles for cellular biochemical circuits in general.

Information processing in bacteria: memory, computation, and statistical physics: a key issues review.

PubMed

Lan, Ganhui; Tu, Yuhai

2016-05-01

Living systems have to constantly sense their external environment and adjust their internal state in order to survive and reproduce. Biological systems, from as complex as the brain to a single E. coli cell, have to process these data in order to make appropriate decisions. How do biological systems sense external signals? How do they process the information? How do they respond to signals? Through years of intense study by biologists, many key molecular players and their interactions have been identified in different biological machineries that carry out these signaling functions. However, an integrated, quantitative understanding of the whole system is still lacking for most cellular signaling pathways, not to say the more complicated neural circuits. To study signaling processes in biology, the key thing to measure is the input-output relationship. The input is the signal itself, such as chemical concentration, external temperature, light (intensity and frequency), and more complex signals such as the face of a cat. The output can be protein conformational changes and covalent modifications (phosphorylation, methylation, etc), gene expression, cell growth and motility, as well as more complex output such as neuron firing patterns and behaviors of higher animals. Due to the inherent noise in biological systems, the measured input-output dependence is often noisy. These noisy data can be analysed by using powerful tools and concepts from information theory such as mutual information, channel capacity, and the maximum entropy hypothesis. This information theory approach has been successfully used to reveal the underlying correlations between key components of biological networks, to set bounds for network performance, and to understand possible network architecture in generating observed correlations. Although the information theory approach provides a general tool in analysing noisy biological data and may be used to suggest possible network architectures in preserving information, it does not reveal the underlying mechanism that leads to the observed input-output relationship, nor does it tell us much about which information is important for the organism and how biological systems use information to carry out specific functions. To do that, we need to develop models of the biological machineries, e.g. biochemical networks and neural networks, to understand the dynamics of biological information processes. This is a much more difficult task. It requires deep knowledge of the underlying biological network-the main players (nodes) and their interactions (links)-in sufficient detail to build a model with predictive power, as well as quantitative input-output measurements of the system under different perturbations (both genetic variations and different external conditions) to test the model predictions to guide further development of the model. Due to the recent growth of biological knowledge thanks in part to high throughput methods (sequencing, gene expression microarray, etc) and development of quantitative in vivo techniques such as various florescence technology, these requirements are starting to be realized in different biological systems. The possible close interaction between quantitative experimentation and theoretical modeling has made systems biology an attractive field for physicists interested in quantitative biology. In this review, we describe some of the recent work in developing a quantitative predictive model of bacterial chemotaxis, which can be considered as the hydrogen atom of systems biology. Using statistical physics approaches, such as the Ising model and Langevin equation, we study how bacteria, such as E. coli, sense and amplify external signals, how they keep a working memory of the stimuli, and how they use these data to compute the chemical gradient. In particular, we will describe how E. coli cells avoid cross-talk in a heterogeneous receptor cluster to keep a ligand-specific memory. We will also study the thermodynamic costs of adaptation for cells to maintain an accurate memory. The statistical physics based approach described here should be useful in understanding design principles for cellular biochemical circuits in general.

Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

PubMed Central

Brezinski, Mark E; Rupnick, Maria

2016-01-01

Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems. PMID:29200743

Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

PubMed

Brezinski, Mark E; Rupnick, Maria

2014-07-01

Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems.

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution.

PubMed

Rothschild, Lynn J

2010-04-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested.

On a biologically inspired topology optimization method

NASA Astrophysics Data System (ADS)

Kobayashi, Marcelo H.

2010-03-01

This work concerns the development of a biologically inspired methodology for the study of topology optimization in engineering and natural systems. The methodology is based on L systems and its turtle interpretation for the genotype-phenotype modeling of the topology development. The topology is analyzed using the finite element method, and optimized using an evolutionary algorithm with the genetic encoding of the L system and its turtle interpretation, as well as, body shape and physical characteristics. The test cases considered in this work clearly show the suitability of the proposed method for the study of engineering and natural complex systems.

Creating biomaterials with spatially organized functionality.

PubMed

Chow, Lesley W; Fischer, Jacob F

2016-05-01

Biomaterials for tissue engineering provide scaffolds to support cells and guide tissue regeneration. Despite significant advances in biomaterials design and fabrication techniques, engineered tissue constructs remain functionally inferior to native tissues. This is largely due to the inability to recreate the complex and dynamic hierarchical organization of the extracellular matrix components, which is intimately linked to a tissue's biological function. This review discusses current state-of-the-art strategies to control the spatial presentation of physical and biochemical cues within a biomaterial to recapitulate native tissue organization and function. © 2016 by the Society for Experimental Biology and Medicine.

Biophysics at the Boundaries: The Next Problem Sets

NASA Astrophysics Data System (ADS)

Skolnick, Malcolm

2009-03-01

The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future biophysicists to fill these roles.

Computing life: Add logos to biology and bios to physics.

PubMed

Kolodkin, Alexey; Simeonidis, Evangelos; Westerhoff, Hans V

2013-04-01

This paper discusses the interrelations between physics and biology. Particularly, we analyse the approaches for reconstructing the emergent properties of physical or biological systems. We propose approaches to scale emergence according to the degree of state-dependency of the system's component properties. Since the component properties of biological systems are state-dependent to a high extent, biological emergence should be considered as very strong emergence - i.e. its reconstruction would require a lot of information about state-dependency of its component properties. However, due to its complexity and volume, this information cannot be handled in the naked human brain, or on the back of an envelope. To solve this problem, biological emergence can be reconstructed in silico based on experimentally determined rate laws and parameter values of the living cell. According to some rough calculations, the silicon human might comprise the mathematical descriptions of around 10(5) interactions. This is not a small number, but taking into account the exponentially increase of computational power, it should not prove to be our principal limitation. The bigger challenges will be located in different areas. For example they may be related to the observer effect - the limitation to measuring a system's component properties without affecting the system. Another obstacle may be hidden in the tradition of "shaving away" all "unnecessary" assumptions (the so-called Occam's razor) that, in fact, reflects the intention to model the system as simply as possible and thus to deem the emergence to be less strong than it possibly is. We argue here that that Occam's razor should be replaced with the law of completeness. Copyright © 2012 Elsevier Ltd. All rights reserved.

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

Topics in Complexity: From Physical to Life Science Systems

NASA Astrophysics Data System (ADS)

Charry, Pedro David Manrique

Complexity seeks to unwrap the mechanisms responsible for collective phenomena across the physical, biological, chemical, economic and social sciences. This thesis investigates real-world complex dynamical systems ranging from the quantum/natural domain to the social domain. The following novel understandings are developed concerning these systems' out-of-equilibrium and nonlinear behavior. Standard quantum techniques show divergent outcomes when a quantum system comprising more than one subunit is far from thermodynamic equilibrium. Abnormal photon inter-arrival times help fulfill the metabolic needs of a terrestrial photosynthetic bacterium. Spatial correlations within incident light can act as a driving mechanism for an organism's adaptation toward more ordered structures. The group dynamics of non-identical objects, whose assembly rules depend on mutual heterogeneity, yield rich transition dynamics between isolation and cohesion, with the cohesion regime reproducing a particular universal pattern commonly found in many real-world systems. Analyses of covert networks reveal collective gender superiority in the connectivity that provides benefits for system robustness and survival. Nodal migration in a network generates complex contagion profiles that lie beyond traditional approaches and yet resemble many modern-day outbreaks.

Is there Complex Trauma Experience typology for Australian's experiencing extreme social disadvantage and low housing stability?

PubMed

Keane, Carol A; Magee, Christopher A; Kelly, Peter J

2016-11-01

Traumatic childhood experiences predict many adverse outcomes in adulthood including Complex-PTSD. Understanding complex trauma within socially disadvantaged populations has important implications for policy development and intervention implementation. This paper examined the nature of complex trauma experienced by disadvantaged individuals using a latent class analysis (LCA) approach. Data were collected through the large-scale Journeys Home Study (N=1682), utilising a representative sample of individuals experiencing low housing stability. Data on adverse childhood experiences, adulthood interpersonal trauma and relevant covariates were collected through interviews at baseline (Wave 1). Latent class analysis (LCA) was conducted to identify distinct classes of childhood trauma history, which included physical assault, neglect, and sexual abuse. Multinomial logistic regression investigated childhood relevant factors associated with class membership such as biological relationship of primary carer at age 14 years and number of times in foster care. Of the total sample (N=1682), 99% reported traumatic adverse childhood experiences. The most common included witnessing of violence, threat/experience of physical abuse, and sexual assault. LCA identified six distinct childhood trauma history classes including high violence and multiple traumas. Significant covariate differences between classes included: gender, biological relationship of primary carer at age 14 years, and time in foster care. Identification of six distinct childhood trauma history profiles suggests there might be unique treatment implications for individuals living in extreme social disadvantage. Further research is required to examine the relationship between these classes of experience, consequent impact on adulthood engagement, and future transitions though homelessness. Copyright © 2016 Elsevier Ltd. All rights reserved.

PREFACE: International & Interdisciplinary Workshop on Novel Phenomena in Integrated Complex Sciences: from Non-living to Living Systems

NASA Astrophysics Data System (ADS)

Yoshimura, Kazuyoshi; Ohta, Hiroto; Murase, Masatoshi; Nishimura, Kazuo

2012-03-01

In this workshop recent advancements in experiments and theories were discussed on magnetism and superconductivity, emergent phenomena in biological material, chemical properties and economic problems of non-living and living systems. The aim of the workshop was to discuss old, but also new problems from a multidisciplinary perspective, and to understand the general features behind diversity in condensed matter physics, experimental chemistry and physics in biology and economic science. The workshop was broadly based, and was titled 'International & Interdisciplinary Workshop on Novel Phenomena in Integrated Complex Sciences from Non-living to Living Systems'. However, the primary focus was on magnetism and superconductivity, and NMR research into strongly correlated electrons. The meeting was held as an ICAM workshop, upon official approval in January 2010. Both young scientists and graduate students were invited. We hope that these young scientists had the chance to talk with invited speakers and organizers on their own interests. We thank the participants who contributed through their presentations, discussions and these papers to the advancement of the subject and our understanding. The proceedings are published here in the Journal of Physics: Conference Series (UK). We thank the International Advisory Committee for their advice and guidance: Evgeny Antipov Moscow State University, Russia Nicholas Curro University of California, Davis, USA Minghu Fang Zhejiang University, China Jurgen Haase University of Leipzig, Germany Takashi Imai McMaster University, Canada Peter Lemmens TU Braunschweig, Germany Herwig Michor Vienna TU, Austria Takamasa Momose University of British Columbia, Canada Raivo Stern NICPB, Estonia Louis Taillefer University of Sherbrooke, Canada Masashi Takigawa University of Tokyo, Japan This workshop was mainly organized by the International Research Unit of Integrated Complex System Science, Kyoto University, and was supported by ICAM (Institute for Complex and Adaptive Matter, USA), Yukawa Institute for Theoretical Physics (Kyoto University), Institute of Economic Research (Kyoto University) and Kyoto University GCOEs (Global Centers Of Excellence: Physics, Chemistry, and Economics). The workshop was also supported by Niki Glass Company Ltd., THAMWAY Corp., TAIYO NIPPON SANSO, and Quantum Design Japan. The Editors and the Organizing Committee, Masatoshi Murase Kyoto University, Japan Kazuo Nishimura Kyoto University, Japan Kazuyoshi Yoshimura Kyoto University, Japan: Conference Chairman and Chief Editor Hiroto Ohta Kyoto University, Tokyo University of A&T, Japan: Conference Secretary Conference Photograph, 14 October 2010 Conference Photograph Conference Poster Conference Poster

Immunology for physicists

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perelson, A.S.; Weisbuch, G.

1997-10-01

The immune system is a complex system of cells and molecules that can provide us with a basic defense against pathogenic organisms. Like the nervous system, the immune system performs pattern recognition tasks, learns, and retains a memory of the antigens that it has fought. The immune system contains more than 10{sup 7} different clones of cells that communicate via cell-cell contact and the secretion of molecules. Performing complex tasks such as learning and memory involves cooperation among large numbers of components of the immune system and hence there is interest in using methods and concepts from statistical physics. Furthermore,more » the immune response develops in time and the description of its time evolution is an interesting problem in dynamical systems. In this paper, the authors provide a brief introduction to the biology of the immune system and discuss a number of immunological problems in which the use of physical concepts and mathematical methods has increased our understanding. {copyright} {ital 1997} {ital The American Physical Society}« less

Darwin's legacy: why biology is not physics, or why evolution has not become a common sense.

PubMed

Singh, Rama S

2011-10-01

Cosmology and evolution together have enabled us to look deep into the past and comprehend evolution-from the big bang to the cosmos, from molecules to humans. Here, I compare the nature of theories in biology and physics and ask why physical theories get accepted by the public without necessarily comprehending them but biological theories do not. Darwin's theory of natural selection, utterly simple in its premises but profound in its consequences, is not accepted widely. Organized religions, and creationists in particularly, have been the major critic of evolution, but not all opposition to evolution comes from organized religions. A great many people, between evolutionary biologists on one hand and creationists on the other, many academics included, who may not be logically opposed to evolution nevertheless do not accept it. This is because the process of and the evidence for evolution are invisible to a nonspecialist, or the theory may look too simple to explain complex traits to some, or because people compare evolution against God and find evolutionary explanations threatening to their beliefs. Considering how evolution affects our lives, including health and the environment to give just two examples, a basic course in evolution should become a required component of all our college and university educational systems.

Modeling Power Systems as Complex Adaptive Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chassin, David P.; Malard, Joel M.; Posse, Christian

2004-12-30

Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We reviewmore » and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.« less

Emergence Processes up to Consciousness Using the Multiplicity Principle and Quantum Physics

NASA Astrophysics Data System (ADS)

Ehresmann, Andrée C.; Vanbremeersch, Jean-Paul

2002-09-01

Evolution is marked by the emergence of new objects and interactions. Pursuing our preceding work on Memory Evolutive Systems (MES; cf. our Internet site), we propose a general mathematical model for this process, based on Category Theory. Its main characteristics is the Multiplicity Principle (MP) which asserts the existence of complex objects with several possible configurations. The MP entails the emergence of non-reducible more and more complex objects (emergentist reductionism). From the laws of Quantum Physics, it follows that the MP is valid for the category of particles and atoms, hence, by complexification, for any natural autonomous anticipatory complex system, such as biological systems up to neural systems, or social systems. Applying the model to the MES of neurons, we describe the emergence of higher and higher cognitive processes and of a semantic memory. Consciousness is characterized by the development of a permanent `personal' memory, the archetypal core, which allows the formation of extended landscapes with an integration of the temporal dimensions.

Surface obstacles in pulsatile flow

NASA Astrophysics Data System (ADS)

Carr, Ian A.; Plesniak, Michael W.

2017-11-01

Flows past obstacles mounted on flat surfaces have been widely studied due to their ubiquity in nature and engineering. For nearly all of these studies, the freestream flow over the obstacle was steady, i.e., constant velocity, unidirectional flow. Unsteady, pulsatile flows occur frequently in biology, geophysics, biomedical engineering, etc. Our study is aimed at extending the comprehensive knowledge base that exists for steady flows to considerably more complex pulsatile flows. Characterizing the vortex and wake dynamics of flows around surface obstacles embedded in pulsatile flows can provide insights into the underlying physics in all wake and junction flows. In this study, we experimentally investigate the wake of two canonical obstacles: a cube and a circular cylinder with an aspect ratio of unity. Our previous studies of a surface-mounted hemisphere in pulsatile flow are used as a baseline for these two new, more complex geometries. Phase-averaged PIV and hot-wire anemometry are used to characterize the dynamics of coherent structures in the wake and at the windward junction of the obstacles. Complex physics occur during the deceleration phase of the pulsatile inflow. We propose a framework for understanding these physics based on self-induced vortex propagation, similar to the phenomena exhibited by vortex rings.

In search of the proper scientific approach: Hayek's views on biology, methodology, and the nature of economics.

PubMed

Beck, Naomi

2009-12-01

Friedrich August von Hayek (1899-1992) is mainly known for his defense of free-market economics and liberalism. His views on science--more specifically on the methodological differences between the physical sciences on the one hand, and evolutionary biology and the social sciences on the other--are less well known. Yet in order to understand, and properly evaluate Hayek's political position, we must look at the theory of scientific method that underpins it. Hayek believed that a basic misunderstanding of the discipline of economics and the complex phenomena with which it deals produced misconceptions concerning its method and goals, which led in turn to the adoption of dangerous policies. The objective of this article is to trace the development of Hayek's views on the nature of economics as a scientific discipline and to examine his conclusions concerning the scope of economic prediction. In doing so, I will first show that Hayek's interest in the natural sciences (especially biology), as well as his interest in epistemology, were central to his thought, dating back to his formative years. I will then emphasize the important place of historical analysis in Hayek's reflections on methodology and examine the reasons for his strong criticism of positivism and socialism. Finally, in the third and fourth sections that constitute the bulk of this article, I will show how Hayek's understanding of the data and goal of the social sciences (which he distinguished from those of the physical sciences), culminated in an analogy that sought to establish economics and evolutionary biology as exemplary complex sciences. I will challenge Hayek's interpretation of this analogy through a comparison with Darwin's views in The Origin of Species, and thus open a door to re-evaluating the theoretical foundations of Hayek's political claims.

Ultrafast electron microscopy in materials science, biology, and chemistry

NASA Astrophysics Data System (ADS)

King, Wayne E.; Campbell, Geoffrey H.; Frank, Alan; Reed, Bryan; Schmerge, John F.; Siwick, Bradley J.; Stuart, Brent C.; Weber, Peter M.

2005-06-01

The use of pump-probe experiments to study complex transient events has been an area of significant interest in materials science, biology, and chemistry. While the emphasis has been on laser pump with laser probe and laser pump with x-ray probe experiments, there is a significant and growing interest in using electrons as probes. Early experiments used electrons for gas-phase diffraction of photostimulated chemical reactions. More recently, scientists are beginning to explore phenomena in the solid state such as phase transformations, twinning, solid-state chemical reactions, radiation damage, and shock propagation. This review focuses on the emerging area of ultrafast electron microscopy (UEM), which comprises ultrafast electron diffraction (UED) and dynamic transmission electron microscopy (DTEM). The topics that are treated include the following: (1) The physics of electrons as an ultrafast probe. This encompasses the propagation dynamics of the electrons (space-charge effect, Child's law, Boersch effect) and extends to relativistic effects. (2) The anatomy of UED and DTEM instruments. This includes discussions of the photoactivated electron gun (also known as photogun or photoelectron gun) at conventional energies (60-200 keV) and extends to MeV beams generated by rf guns. Another critical aspect of the systems is the electron detector. Charge-coupled device cameras and microchannel-plate-based cameras are compared and contrasted. The effect of various physical phenomena on detective quantum efficiency is discussed. (3) Practical aspects of operation. This includes determination of time zero, measurement of pulse-length, and strategies for pulse compression. (4) Current and potential applications in materials science, biology, and chemistry. UEM has the potential to make a significant impact in future science and technology. Understanding of reaction pathways of complex transient phenomena in materials science, biology, and chemistry will provide fundamental knowledge for discovery-class science.

Nonreconstruction Options for Treating Medial Ulnar Collateral Ligament Injuries of the Elbow in Overhead Athletes.

PubMed

Clark, Nicholas J; Desai, Vishal S; Dines, Joshua D; Morrey, Mark E; Camp, Christopher L

2018-03-01

This review aims to describe the nonreconstructive options for treating ulnar collateral ligament (UCL) injuries ranging from nonoperative measures, including physical therapy and biologic injections, to ligament repair with and without augmentation. Nonoperative options for UCL injuries include guided physical therapy and biologic augmentation with platelet-rich plasma (PRP). In some patients, repair of the UCL has shown promising return to sport rates by using modern suture and suture anchor techniques. Proximal avulsion injuries have shown the best results after repair. Currently, there is growing interest in augmentation of UCL repair with an internal brace. The treatment of UCL injuries involves complex decision making. UCL reconstruction remains the gold standard for attritional injuries and complete tears, which occur commonly in professional athletes. However, nonreconstructive options have shown promising results for simple avulsion or partial thickness UCL injuries. Future research comparing reconstructive versus nonreconstructive options is necessary.

From Rivers to Oceans and Back: Linking Models to Encompass the Full Salmon Life Cycle

NASA Astrophysics Data System (ADS)

Danner, E.; Hendrix, N.; Martin, B.; Lindley, S. T.

2016-02-01

Pacific salmon are a promising study subject for investigating the linkages between freshwater and coastal ocean ecosystems. Salmon use a wide range of habitats throughout their life cycle as they move with water from mountain streams, mainstem rivers, estuaries, bays, and coastal oceans, with adult fish swimming back through the same migration route they took as juveniles. Conditions in one habitat can have growth and survival consequences that manifest in the following habitat, so is key that full life cycle models are used to further our understanding salmon population dynamics. Given the wide range of habitats and potential stressors, this approach requires the coordination of a multidisciplinary suite of physical and biological models, including climate, hydrologic, hydraulic, food web, circulation, bioenergetic, and ecosystem models. Here we present current approaches to linking physical and biological models that capture the foundational drivers for salmon in complex and dynamic systems.

Driftcretions: The legacy impacts of driftwood on shoreline morphology

NASA Astrophysics Data System (ADS)

Kramer, Natalie; Wohl, Ellen

2015-07-01

This research demonstrates how vegetation interacts with physical processes to govern landscape development. We quantify and describe interactions among driftwood, sedimentation, and vegetation for Great Slave Lake, which is used as proxy for shoreline dynamics and landforms before deforestation and wood removal along major waterways. We introduce driftcretion to describe large, persistent concentrations of driftwood that interact with vegetation and sedimentation to influence shoreline evolution. We report the volume and distribution of driftwood along shorelines, the morphological impacts of driftwood delivery throughout the Holocene, and rates of driftwood accretion. Driftcretions facilitate the formation of complex, diverse morphologies that increase biological productivity and organic carbon capture and buffer against erosion. Driftcretions should be common on shorelines receiving a large wood supply and with processes which store wood permanently. We encourage others to work in these depositional zones to understand the physical and biological impacts of large wood export from river basins.

The Photo-Physics of Polythiophene Nanoparticles for Biological Applications.

PubMed

Bargigia, Ilaria; Zucchetti, Elena; Srimath Kandada, Ajay Ram; Moreira, Miguel; Bossio, Caterina; Wong, Walter; Miranda, Paulo; Decuzzi, Paolo; Soci, Cesare; D'Andrea, Cosimo; Lanzani, Guglielmo

2018-05-01

In this work the photo-physics of poly(3-hexyltiophene) nanoparticles (NPs) is investigated in the context of their biological applications. The NPs made as colloidal suspensions in aqueous buffers present a distinct absorption band in the low energy region. Based on systematic analysis of absorption and transient absorption spectra taken under different pH conditions, this band is associated to charge transfer states generated by the polarization of loosely bound polymer chains and originated from complexes formed with electron withdrawing species. Importantly, the ground state depletion of these states upon photo-excitation is active even in the microsecond timescales, suggesting that they act as precursor states for long-living polarons which could be beneficial for cellular stimulation. Preliminary results of transient absorption microscopy of NPs internalized within the cells reveal the presence of long-living species, further substantiating their relevance in bio-interfaces. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biodegradability of Plastics: Challenges and Misconceptions.

PubMed

Kubowicz, Stephan; Booth, Andy M

2017-11-07

Plastics are one of the most widely used materials and, in most cases, they are designed to have long life times. Thus, plastics contain a complex blend of stabilizers that prevent them from degrading too quickly. Unfortunately, many of the most advantageous properties of plastics such as their chemical, physical and biological inertness and durability present challenges when plastic is released into the environment. Common plastics such as polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyethylene terephthalate (PET) are extremely persistent in the environment, where they undergo very slow fragmentation (projected to take centuries) into small particles through photo-, physical, and biological degradation processes 1 . The fragmentation of the material into increasingly smaller pieces is an unavoidable stage of the degradation process. Ultimately, plastic materials degrade to micron-sized particles (microplastics), which are persistent in the environment and present a potential source of harm for organisms.

Evolution: like any other science it is predictable.

PubMed

Morris, Simon Conway

2010-01-12

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology ('evolution explains evolution'). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.

Evolution: like any other science it is predictable

PubMed Central

Conway Morris, Simon

2010-01-01

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein. PMID:20008391

Physical and biological properties of U. S. standard endotoxin EC after exposure to ionizing radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Csako, G.; Elin, R.J.; Hochstein, H.D.

Techniques that reduce the toxicity of bacterial endotoxins are useful for studying the relationship between structure and biological activity. We used ionizing radiation to detoxify a highly refined endotoxin preparation. U.S. standard endotoxin EC. Dose-dependent changes occurred by exposure to /sup 60/Co-radiation in the physical properties and biological activities of the endotoxin. Sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis showed gradual loss of the polysaccharide components (O-side chain and R-core) from the endotoxin molecules. In contrast, although endotoxin revealed a complex absorption pattern in the UV range, radiation treatment failed to modify that pattern. Dose-related destruction of the primary toxic component,more » lipid A, was suggested by the results of activity tests: both the pyrogenicity and limulus reactivity of the endotoxin were destroyed by increasing doses of radiation. The results indicate that the detoxification is probably due to multiple effects of the ionizing radiation on bacterial lipopolysaccharides, and the action involves (i) the destruction of polysaccharide moieties and possibly (ii) the alteration of lipid A component of the endotoxin molecule.« less

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

PubMed

Solovyev, Alexey; Mikheev, Maxim; Zhou, Leming; Dutta-Moscato, Joyeeta; Ziraldo, Cordelia; An, Gary; Vodovotz, Yoram; Mi, Qi

2010-01-01

Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

Education and Training in the Social, Behavioral, and Economic Sciences: A Plan of Action. A Report to the National Science Foundation.

ERIC Educational Resources Information Center

Levine, Felice J.; Abler, Ronald F.; Rosich, Katherine J.

2004-01-01

Over the last quarter of a century, the world has undergone rapid change. Almost every aspect of human life is more complex and interdependent, requiring knowledge of human and social systems as well as physical and biological systems. The social, behavioral, and economic (SBE) sciences contribute penetrating insights on such issues as the causes…

Army Ecosystem Management Policy Study

DTIC Science & Technology

1997-03-01

natural resources. A new generation of environmental issues is now upon us, defined by greater political, economic, social , and even cultural complexity...be established according to physical and biological criteria, and should account for the regional political, social , economic, and cultural context...speaks to what is known or what is knowable about a problem or situation. This determination is heavily influenced by social values and perceptions. We

BAC sequencing using pooled methods.

PubMed

Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

2015-01-01

Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

A journey from reductionist to systemic cell biology aboard the schooner Tara.

PubMed

Karsenti, Eric

2012-07-01

In this essay I describe my personal journey from reductionist to systems cell biology and describe how this in turn led to a 3-year sea voyage to explore complex ocean communities. In describing this journey, I hope to convey some important principles that I gleaned along the way. I realized that cellular functions emerge from multiple molecular interactions and that new approaches borrowed from statistical physics are required to understand the emergence of such complex systems. Then I wondered how such interaction networks developed during evolution. Because life first evolved in the oceans, it became a natural thing to start looking at the small organisms that compose the plankton in the world's oceans, of which 98% are … individual cells-hence the Tara Oceans voyage, which finished on 31 March 2012 in Lorient, France, after a 60,000-mile around-the-world journey that collected more than 30,000 samples from 153 sampling stations.

Nonlinear mechanics of hybrid polymer networks that mimic the complex mechanical environment of cells

NASA Astrophysics Data System (ADS)

Jaspers, Maarten; Vaessen, Sarah L.; van Schayik, Pim; Voerman, Dion; Rowan, Alan E.; Kouwer, Paul H. J.

2017-05-01

The mechanical properties of cells and the extracellular environment they reside in are governed by a complex interplay of biopolymers. These biopolymers, which possess a wide range of stiffnesses, self-assemble into fibrous composite networks such as the cytoskeleton and extracellular matrix. They interact with each other both physically and chemically to create a highly responsive and adaptive mechanical environment that stiffens when stressed or strained. Here we show that hybrid networks of a synthetic mimic of biological networks and either stiff, flexible and semi-flexible components, even very low concentrations of these added components, strongly affect the network stiffness and/or its strain-responsive character. The stiffness (persistence length) of the second network, its concentration and the interaction between the components are all parameters that can be used to tune the mechanics of the hybrids. The equivalence of these hybrids with biological composites is striking.

On residual stresses and homeostasis: an elastic theory of functional adaptation in living matter.

PubMed

Ciarletta, P; Destrade, M; Gower, A L

2016-04-26

Living matter can functionally adapt to external physical factors by developing internal tensions, easily revealed by cutting experiments. Nonetheless, residual stresses intrinsically have a complex spatial distribution, and destructive techniques cannot be used to identify a natural stress-free configuration. This work proposes a novel elastic theory of pre-stressed materials. Imposing physical compatibility and symmetry arguments, we define a new class of free energies explicitly depending on the internal stresses. This theory is finally applied to the study of arterial remodelling, proving its potential for the non-destructive determination of the residual tensions within biological materials.

Advances in modelling of biomimetic fluid flow at different scales

PubMed Central

2011-01-01

The biomimetic flow at different scales has been discussed at length. The need of looking into the biological surfaces and morphologies and both geometrical and physical similarities to imitate the technological products and processes has been emphasized. The complex fluid flow and heat transfer problems, the fluid-interface and the physics involved at multiscale and macro-, meso-, micro- and nano-scales have been discussed. The flow and heat transfer simulation is done by various CFD solvers including Navier-Stokes and energy equations, lattice Boltzmann method and molecular dynamics method. Combined continuum-molecular dynamics method is also reviewed. PMID:21711847

Protein-Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

NASA Astrophysics Data System (ADS)

Rusmerryani, Micke; Takasu, Masako; Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

Proteins usually perform their biological functions by forming a complex with other proteins. It is very important to study the protein-protein interactions since these interactions are crucial in many processes of a living organism. In this study, we develop a coarse grained model to simulate protein complex in liquid system. We carry out molecular dynamics simulations with topology-based potential interactions to simulate dynamical properties of Pseudomonas Aeruginosa azurin complex systems. Azurin is known to play an essential role as an anticancer agent and bind many important intracellular molecules. Some physical properties are monitored during simulation time to get a better understanding of the influence of protein-protein interactions to the azurin complex dynamics. These studies will provide valuable insights for further investigation on protein-protein interactions in more realistic system.

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

PREFACE: Scales of understanding in biological development Scales of understanding in biological development

NASA Astrophysics Data System (ADS)

Newman, Timothy

2011-08-01

The development of an adult organism from a fertilized egg remains one of the deep mysteries of biology. Great strides have been made in the past three decades, primarily through ever more sophisticated genetic analyses and the advent of live-cell imaging, yet the underlying principles governing development are elusive. Recently, a new generation of biological physicists has entered the field, attracted by the hallmarks of development— coordinated dynamics and pattern formation arising from cell-cell interactions—which reflect tantalizing analogs with many-body systems in condensed matter physics and related fields. There have been corresponding influxes of researchers from other quantitative disciplines. With new workers come new questions and foci at different scales in space, time and complexity. The reductionist philosophy of developmental genetics has become increasingly complemented by a search for effective mechanisms at higher scales, a strategy which has a proven track record of success in the study of complex systems in physics. Are there new and universal mechanisms of development, supra-genetic in nature, waiting to be discovered by focusing on higher scales, or is development fundamentally the intricately scripted unfolding of complex genetic instructions? In this special focus issue of Physical Biology, we present cutting-edge research into embryo development from a broad spectrum of groups representing cell and developmental biology, biological physics, bioengineering and biomathematics. We are provided with a sense of how this multidisciplinary community views the fundamental issue of scale in development and are given some excellent examples of how we can bridge these scales through interdisciplinary collaboration, in order to create new levels of understanding. We start with two reviews which will provide newcomers with a guide to some of the outstanding questions in the field. Winklbauer and Müller use the phenomenon of mesoderm spreading as a platform to discuss the fascinating challenge of connecting cell-level behaviours to tissue-scale dynamics, thereby putting meat on the bones of traditional physical metaphors of 'the embryonic tissue as a material'. A fresh look at natural variation in embryonic phenotypes through the lens of physics, especially mechanics, is provided by von Dassow and Davidson. They stress the importance of environmental scales in providing both physical challenges and an evolutionary backdrop for robust development. The next two papers are concerned with the crucial role of signalling in morphogenesis. Zartman et al study in detail a stage of oogenesis in Drosophila, and show how quantitative experimental determination of pattern formation can be used as a stringent test of proposed underlying molecular mechanisms; in turn, they show how such selected mechanisms can thereafter be tested by newly designed experiments. Streichan et al consider collective cell motion in the zebrafish embryo. They propose an elegant theoretical mechanism to explain how directed collective cell motion can be generated in a uniform signalling landscape through a non-linear chemotactic feedback loop, and propose experimental tests of this idea. The next two papers describe state-of-the-art spatio-temporal quantification of whole embryo dynamics with cell-level resolution. Fernandez-Gonzalez and Zallen study the fascinating phenomenon of cell surface oscillations during axis elongation in Drosophila. They use a newly designed computer algorithm to measure spatio-temporal statistics of the oscillations and connect this information to intracellular actomyosin dynamics. Szabó et al study extracellular matrix (ECM) dynamics during primitive streak extension in the avian embryo. Using computer tracking and analysis they are able to measure spatial and temporal correlations of the ECM during development and use this data to inform the crucial, yet poorly understood, role of cell-ECM interactions. The last two papers are companion articles by Sandersius et al. The first paper describes the integration of active subcellular dynamics into an existing multicellular simulation algorithm. The resulting algorithm, which is parameterized at length and time scales of microns and seconds, is capable of reproducing various experimentally observed phenotypes at significantly higher scales, namely large-strain cell stretching, effective viscosity of embryonic epithelia and streaming patterns of collective cell motion within tissues. The second paper uses this new algorithm to quantitatively test the hypothesis that a dipolar arrangement of chemotactic sources is capable of driving primitive streak formation in amniotes. The hypothesis is found to be consistent with experimental data on cell movement patterns and quantitative estimates are given for the robustness of the chemotaxis mechanism. Is the simplest model of an embryo an embryo? Alternatively, are there higher scales of understanding that will provide predictive and powerful new insights into development? We hope this special focus issue of Physical Biology will provide a snapshot of how quantitative and interdisciplinary approaches are helping to answer these fundamental questions.

A comparison of LMC and SDL complexity measures on binomial distributions

NASA Astrophysics Data System (ADS)

Piqueira, José Roberto C.

2016-02-01

The concept of complexity has been widely discussed in the last forty years, with a lot of thinking contributions coming from all areas of the human knowledge, including Philosophy, Linguistics, History, Biology, Physics, Chemistry and many others, with mathematicians trying to give a rigorous view of it. In this sense, thermodynamics meets information theory and, by using the entropy definition, López-Ruiz, Mancini and Calbet proposed a definition for complexity that is referred as LMC measure. Shiner, Davison and Landsberg, by slightly changing the LMC definition, proposed the SDL measure and the both, LMC and SDL, are satisfactory to measure complexity for a lot of problems. Here, SDL and LMC measures are applied to the case of a binomial probability distribution, trying to clarify how the length of the data set implies complexity and how the success probability of the repeated trials determines how complex the whole set is.

WE-DE-202-02: Are Track Structure Simulations Truly Needed for Radiobiology at the Cellular and Tissue Levels?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, R.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, S.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less

On Wiener polarity index of bicyclic networks.

PubMed

Ma, Jing; Shi, Yongtang; Wang, Zhen; Yue, Jun

2016-01-11

Complex networks are ubiquitous in biological, physical and social sciences. Network robustness research aims at finding a measure to quantify network robustness. A number of Wiener type indices have recently been incorporated as distance-based descriptors of complex networks. Wiener type indices are known to depend both on the network's number of nodes and topology. The Wiener polarity index is also related to the cluster coefficient of networks. In this paper, based on some graph transformations, we determine the sharp upper bound of the Wiener polarity index among all bicyclic networks. These bounds help to understand the underlying quantitative graph measures in depth.

Fractal morphometry of cell complexity.

PubMed

Losa, Gabriele A

2002-01-01

Irregularity and self-similarity under scale changes are the main attributes of the morphological complexity of both normal and abnormal cells and tissues. In other words, the shape of a self-similar object does not change when the scale of measurement changes, because each part of it looks similar to the original object. However, the size and geometrical parameters of an irregular object do differ when it is examined at increasing resolution, which reveals more details. Significant progress has been made over the past three decades in understanding how irregular shapes and structures in the physical and biological sciences can be analysed. Dominant influences have been the discovery of a new practical geometry of Nature, now known as fractal geometry, and the continuous improvements in computation capabilities. Unlike conventional Euclidean geometry, which was developed to describe regular and ideal geometrical shapes which are practically unknown in nature, fractal geometry can be used to measure the fractal dimension, contour length, surface area and other dimension parameters of almost all irregular and complex biological tissues. We have used selected examples to illustrate the application of the fractal principle to measuring irregular and complex membrane ultrastructures of cells at specific functional and pathological stage.

Trans-algorithmic nature of learning in biological systems.

PubMed

Shimansky, Yury P

2018-05-02

Learning ability is a vitally important, distinctive property of biological systems, which provides dynamic stability in non-stationary environments. Although several different types of learning have been successfully modeled using a universal computer, in general, learning cannot be described by an algorithm. In other words, algorithmic approach to describing the functioning of biological systems is not sufficient for adequate grasping of what is life. Since biosystems are parts of the physical world, one might hope that adding some physical mechanisms and principles to the concept of algorithm could provide extra possibilities for describing learning in its full generality. However, a straightforward approach to that through the so-called physical hypercomputation so far has not been successful. Here an alternative approach is proposed. Biosystems are described as achieving enumeration of possible physical compositions though random incremental modifications inflicted on them by active operating resources (AORs) in the environment. Biosystems learn through algorithmic regulation of the intensity of the above modifications according to a specific optimality criterion. From the perspective of external observers, biosystems move in the space of different algorithms driven by random modifications imposed by the environmental AORs. A particular algorithm is only a snapshot of that motion, while the motion itself is essentially trans-algorithmic. In this conceptual framework, death of unfit members of a population, for example, is viewed as a trans-algorithmic modification made in the population as a biosystem by environmental AORs. Numerous examples of AOR utilization in biosystems of different complexity, from viruses to multicellular organisms, are provided.

Fort Collins Science Center Ecosystem Dynamics Branch

USGS Publications Warehouse

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

Modelling fungal growth in heterogeneous soil: analyses of the effect of soil physical structure on fungal community dynamics

NASA Astrophysics Data System (ADS)

Falconer, R.; Radoslow, P.; Grinev, D.; Otten, W.

2009-04-01

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for community dynamics are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects fungal colony dynamics and also how fungal dynamics affect soil structure. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, fractal dimension, and the connectivity of the pore volume. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on microbial dynamics by qualifying biomass abundances and distributions. We demonstrate how soil structure can critically affect fungal species interactions with consequences for biological control and fungal biodiversity.

Biological life-support systems for Mars mission.

PubMed

Gitelson, J I

1992-01-01

Mars mission like the Lunar base is the first venture to maintain human life beyond earth biosphere. So far, all manned space missions including the longest ones used stocked reserves and can not be considered egress from biosphere. Conventional path proposed by technology for Martian mission LSS is to use physical-chemical approaches proved by the experience of astronautics. But the problem of man living beyond the limits of the earth biosphere can be fundamentally solved by making a closed ecosystem for him. The choice optimum for a Mars mission LSS can be substantiated by comparing the merits and demerits of physical-chemical and biological principles without ruling out possible compromise between them. The work gives comparative analysis of ecological and physical-chemical principles for LSS. Taking into consideration universal significance of ecological problems with artificial LSS as a particular case of their solution, complexity and high cost of large-scale experiments with manned LSS, it would be expedient for these works to have the status of an International Program open to be joined. A program of making artificial biospheres based on preceding experience and analysis of current situation is proposed.

Simulating biological processes: stochastic physics from whole cells to colonies.

PubMed

Earnest, Tyler M; Cole, John A; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a 'minimal cell'. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

Simulating biological processes: stochastic physics from whole cells to colonies

NASA Astrophysics Data System (ADS)

Earnest, Tyler M.; Cole, John A.; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a ‘minimal cell’. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Authors, Various

Planning a rational energy future requires anticipating the environmental consequences of various technologies. This is difficult to do with precision as the effects of pollutants are often determined by interactions between and among complex physical (abiotic) and biological (biotic) systems. A given pollutant may affect human beings through direct exposure or indirectly through inducing changes to biological systems which humans need to utilize. The concentration of a toxin in the food chain or the destruction of organisms necessary for the maintenance of high quality water are examples of indirect effects. Pollutants can be transformed and/or degraded as they establish residencemore » in various components of an ecosystem. Anticipation and amelioration of pollutant effects involves the integration of a vast range of data. This data includes: (1) physical and chemical characterization cf the pollutant as it enters the environment; (2) determining effects on the various components (biotic and abiotic) within the context of the functioning ecosystem of interest; (3) transformation in movements and/or degradation of the pollutant within that ecosystem and within specific organisms and physical components; and (4) determining a detailed biochemical and biological picture of the interactions of pollutants with particular organisms and/or their cellular components judged salient for various processes. The major programs described below are designed to answer parts of the above fundamental questions relevant to pollutants generated by energy related technologies. Their emphasis is on anticipating consequences to the biological components of various ecosystems. The work ranges from studies involving parts of a single cell (the membranes) to studies involving the whole ecosystem (in the pelagic zone of a lake). The programs take advantage of expertise and technical abilities present at LBL. Two small exploratory projects which were of brief duration and not related to anticipating biological effects of pollutants are included in this section. They concern geothermal technology and its improvement using techniques based on organic and physical properties of certain materials.« less

God, the Devil, and Darwin - A Critique of Intelligent Design Theory

NASA Astrophysics Data System (ADS)

Shanks, Niall

2007-03-01

In the last fifteen years a controversial new theory of the origins of biological complexity and the nature of the universe has been fomenting bitter debates in education and science policy across North America, Europe, and Australia. Backed by intellectuals at respectable universities, Intelligent Design theory (ID) proposes an alternative to accepted accounts of evolutionary theory: that life is so complex, and that the universe is so fine-tuned for the appearance of life, that the only plausible explanation is the existence of an intelligent designer. For many ID theorists, the designer is taken to be the god of Christianity. Niall Shanks has written the first accessible introduction to, and critique of, this controversial new intellectual movement. Shanks locates the growth of ID in the last two decades of the twentieth century in the growing influence of the American religious right. But as he shows, its roots go back beyond Aquinas to Ancient Greece. After looking at the historical roots of ID, Shanks takes a hard look at its intellectual underpinnings, discussing modern understandings of thermodynamics, and how self-organizing processes lead to complex physical, chemical, and biological systems. He considers cosmological arguments for ID rooted in so-called "anthropic coincidences" and also tackles new biochemical arguments for ID based on "irreducible biological complexity." Throughout he shows how arguments for ID lack cohesion, rest on errors and unfounded suppositions, and generally are grossly inferior to evolutionary explanations. While ID has been proposed as a scientific alternative to evolutionary biology, Shanks argues that ID is in fact "old creationist wine in new designer label bottles" and moreover is a serious threat to the scientific and democratic values that are our cultural and intellectual inheritance from the Enlightenment.

Investigating Processes of Materials Formation via Liquid Phase and Cryogenic TEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Yoreo, James J.; Sommerdijk, Nico

2016-06-14

The formation of materials in solutions is a widespread phenomenon in synthetic, biological and geochemical systems, occurring through dynamic processes of nucleation, self-assembly, crystal growth, and coarsening. The recent advent of liquid phase TEM and advances in cryogenic TEM are transforming our understanding of these phenomena by providing new insights into the underlying physical and chemical mechanisms. The techniques have been applied to metallic and semiconductor nanoparticles, geochemical and biological minerals, electrochemical systems, macromolecular complexes, and selfassembling systems, both organic and inorganic. New instrumentation and methodologies currently on the horizon promise new opportunities for advancing the science of materials synthesis.

Finite Dimensional Approximations for Continuum Multiscale Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berlyand, Leonid

2017-01-24

The completed research project concerns the development of novel computational techniques for modeling nonlinear multiscale physical and biological phenomena. Specifically, it addresses the theoretical development and applications of the homogenization theory (coarse graining) approach to calculation of the effective properties of highly heterogenous biological and bio-inspired materials with many spatial scales and nonlinear behavior. This theory studies properties of strongly heterogeneous media in problems arising in materials science, geoscience, biology, etc. Modeling of such media raises fundamental mathematical questions, primarily in partial differential equations (PDEs) and calculus of variations, the subject of the PI’s research. The focus of completed researchmore » was on mathematical models of biological and bio-inspired materials with the common theme of multiscale analysis and coarse grain computational techniques. Biological and bio-inspired materials offer the unique ability to create environmentally clean functional materials used for energy conversion and storage. These materials are intrinsically complex, with hierarchical organization occurring on many nested length and time scales. The potential to rationally design and tailor the properties of these materials for broad energy applications has been hampered by the lack of computational techniques, which are able to bridge from the molecular to the macroscopic scale. The project addressed the challenge of computational treatments of such complex materials by the development of a synergistic approach that combines innovative multiscale modeling/analysis techniques with high performance computing.« less

Bridging Physics and Biology Using Resistance and Axons

ERIC Educational Resources Information Center

Dyer, Joshua M.

2014-01-01

When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics. A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite…

Predicting Salmonella populations from biological, chemical, and physical indicators in Florida surface waters.

PubMed

McEgan, Rachel; Mootian, Gabriel; Goodridge, Lawrence D; Schaffner, Donald W; Danyluk, Michelle D

2013-07-01

Coliforms, Escherichia coli, and various physicochemical water characteristics have been suggested as indicators of microbial water quality or index organisms for pathogen populations. The relationship between the presence and/or concentration of Salmonella and biological, physical, or chemical indicators in Central Florida surface water samples over 12 consecutive months was explored. Samples were taken monthly for 12 months from 18 locations throughout Central Florida (n = 202). Air and water temperature, pH, oxidation-reduction potential (ORP), turbidity, and conductivity were measured. Weather data were obtained from nearby weather stations. Aerobic plate counts and most probable numbers (MPN) for Salmonella, E. coli, and coliforms were performed. Weak linear relationships existed between biological indicators (E. coli/coliforms) and Salmonella levels (R(2) < 0.1) and between physicochemical indicators and Salmonella levels (R(2) < 0.1). The average rainfall (previous day, week, and month) before sampling did not correlate well with bacterial levels. Logistic regression analysis showed that E. coli concentration can predict the probability of enumerating selected Salmonella levels. The lack of good correlations between biological indicators and Salmonella levels and between physicochemical indicators and Salmonella levels shows that the relationship between pathogens and indicators is complex. However, Escherichia coli provides a reasonable way to predict Salmonella levels in Central Florida surface water through logistic regression.

Predicting Salmonella Populations from Biological, Chemical, and Physical Indicators in Florida Surface Waters

PubMed Central

McEgan, Rachel; Mootian, Gabriel; Goodridge, Lawrence D.; Schaffner, Donald W.

2013-01-01

Coliforms, Escherichia coli, and various physicochemical water characteristics have been suggested as indicators of microbial water quality or index organisms for pathogen populations. The relationship between the presence and/or concentration of Salmonella and biological, physical, or chemical indicators in Central Florida surface water samples over 12 consecutive months was explored. Samples were taken monthly for 12 months from 18 locations throughout Central Florida (n = 202). Air and water temperature, pH, oxidation-reduction potential (ORP), turbidity, and conductivity were measured. Weather data were obtained from nearby weather stations. Aerobic plate counts and most probable numbers (MPN) for Salmonella, E. coli, and coliforms were performed. Weak linear relationships existed between biological indicators (E. coli/coliforms) and Salmonella levels (R2 < 0.1) and between physicochemical indicators and Salmonella levels (R2 < 0.1). The average rainfall (previous day, week, and month) before sampling did not correlate well with bacterial levels. Logistic regression analysis showed that E. coli concentration can predict the probability of enumerating selected Salmonella levels. The lack of good correlations between biological indicators and Salmonella levels and between physicochemical indicators and Salmonella levels shows that the relationship between pathogens and indicators is complex. However, Escherichia coli provides a reasonable way to predict Salmonella levels in Central Florida surface water through logistic regression. PMID:23624476

Estimating Escherichia coli loads in streams based on various physical, chemical, and biological factors

PubMed Central

Dwivedi, Dipankar; Mohanty, Binayak P.; Lesikar, Bruce J.

2013-01-01

Microbes have been identified as a major contaminant of water resources. Escherichia coli (E. coli) is a commonly used indicator organism. It is well recognized that the fate of E. coli in surface water systems is governed by multiple physical, chemical, and biological factors. The aim of this work is to provide insight into the physical, chemical, and biological factors along with their interactions that are critical in the estimation of E. coli loads in surface streams. There are various models to predict E. coli loads in streams, but they tend to be system or site specific or overly complex without enhancing our understanding of these factors. Hence, based on available data, a Bayesian Neural Network (BNN) is presented for estimating E. coli loads based on physical, chemical, and biological factors in streams. The BNN has the dual advantage of overcoming the absence of quality data (with regards to consistency in data) and determination of mechanistic model parameters by employing a probabilistic framework. This study evaluates whether the BNN model can be an effective alternative tool to mechanistic models for E. coli loads estimation in streams. For this purpose, a comparison with a traditional model (LOADEST, USGS) is conducted. The models are compared for estimated E. coli loads based on available water quality data in Plum Creek, Texas. All the model efficiency measures suggest that overall E. coli loads estimations by the BNN model are better than the E. coli loads estimations by the LOADEST model on all the three occasions (three-fold cross validation). Thirteen factors were used for estimating E. coli loads with the exhaustive feature selection technique, which indicated that six of thirteen factors are important for estimating E. coli loads. Physical factors included temperature and dissolved oxygen; chemical factors include phosphate and ammonia; biological factors include suspended solids and chlorophyll. The results highlight that the LOADEST model estimates E. coli loads better in the smaller ranges, whereas the BNN model estimates E. coli loads better in the higher ranges. Hence, the BNN model can be used to design targeted monitoring programs and implement regulatory standards through TMDL programs. PMID:24511166

Physics of Cell Adhesion Failure and Human Diseases

NASA Astrophysics Data System (ADS)

Family, Fereydoon

Emergent phenomena in living systems, including your ability to read these lines, do not obviously follow as a consequence of the fundamental laws of physics. Understanding the physics of living systems clearly falls outside the conventional boundaries of scientific disciplines and requires a collaborative, multidisciplinary approach. Here I will discuss how theoretical and computational techniques from statistical physics can be used to make progress in explaining the physical mechanisms that underlie complex biological phenomena, including major diseases. In the specific cases of macular degeneration and cancer that we have studied recently, we find that the breakdown of the mechanical stability in the local tissue structure caused by weakening of the cell-cell adhesion plays a key role in the initiation and progression of the disease. This finding can help in the development of new therapies that would prevent or halt the initiation and progression of these diseases.

Sensor Abstractions to Support Many-Robot Systems

DTIC Science & Technology

1993-04-01

the behaviors of the social insects: ants, bees, and termites ; the observed aggregate behaviors exhibit a greater complexity, while the individual...applicability -’f" togies from biology (hjrdirg, ec!"x’-oig, iiununc system and pheromone mechanisms) and physics (entropy, temperature, pressure...in [17-19]. Pheromones provide an important example of animals arranging their environment to, for example, help moths find mates, or to help a colony

Tell Me How to Do This Thing Called Design! Practical Application of Complexity Theory to Military Operations

DTIC Science & Technology

2011-04-08

into how economics, information theory and computer science, psychology, sociology, evolutionary biology, physics (quantum mechanics) and cosmology ...include knowledge and definition of “self” (as “self” is part of the environment) and the shared experience and perspective of others  That...including information, entropy, quantum behavior, and cosmological progress In short I assume the above and therefore my recommendations could be

[Medical and biologic aspects of regulation and evaluation of microclimate: results and prospects of further studies].

PubMed

Afanas'eva, R F

2008-01-01

The article deals with basic points concerning influence of microclimate on humans and tasks of its regulation in contemporary conditions. The authors described universality of microclimate from viewpoint of producing functional state and health state of human, so microclimate should be assessed consistently and systematically through all aspects of its influence, with complex approach to evaluation (clothing, physical activity, etc.).

Inference, simulation, modeling, and analysis of complex networks, with special emphasis on complex networks in systems biology

NASA Astrophysics Data System (ADS)

Christensen, Claire Petra

Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author's own publications have contributed network inference, simulation, modeling, and analysis methods to the much larger body of work in systems biology, and indeed, in network science. The aim of this thesis is therefore twofold: to present this original work in the historical context of network science, but also to provide sufficient review and reference regarding complex systems (with an emphasis on complex networks in systems biology) and tools and techniques for their inference, simulation, analysis, and modeling, such that the reader will be comfortable in seeking out further information on the subject. The review-like Chapters 1, 2, and 4 are intended to convey the co-evolution of network science and the slow but noticeable breakdown of boundaries between disciplines in academia as research and comparison of diverse systems has brought to light the shared properties of these systems. It is the author's hope that theses chapters impart some sense of the remarkable and rapid progress in complex systems research that has led to this unprecedented academic synergy. Chapters 3 and 5 detail the author's original work in the context of complex systems research. Chapter 3 presents the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. These networks are then analyzed from a graph theoretical perspective, and their biological viability is critiqued by comparing the networks' graph theoretical properties to those of other biological systems. The results of topological perturbation analyses revealing commonalities in behavior at multiple levels of complexity are also presented, and are shown to be an invaluable means by which to ascertain the level of complexity to which the network inference process is robust to noise. Chapter 5 outlines a learning algorithm for the development of a realistic, evolving social network (a city) into which a disease is introduced. The results of simulations in populations spanning two orders of magnitude are compared to prevaccine era measles data for England and Wales and demonstrate that the simulations are able to capture the quantitative and qualitative features of epidemics in populations as small as 10,000 people. The work presented in Chapter 5 validates the utility of network simulation in concurrently probing contact network dynamics and disease dynamics.

Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review.

PubMed

Boyd, Philip W; Collins, Sinead; Dupont, Sam; Fabricius, Katharina; Gattuso, Jean-Pierre; Havenhand, Jonathan; Hutchins, David A; Riebesell, Ulf; Rintoul, Max S; Vichi, Marcello; Biswas, Haimanti; Ciotti, Aurea; Gao, Kunshan; Gehlen, Marion; Hurd, Catriona L; Kurihara, Haruko; McGraw, Christina M; Navarro, Jorge M; Nilsson, Göran E; Passow, Uta; Pörtner, Hans-Otto

2018-06-01

Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process-oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation. © 2018 John Wiley & Sons Ltd.

The social neuroscience and the theory of integrative levels.

PubMed

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not.

The social neuroscience and the theory of integrative levels

PubMed Central

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not. PMID:26578909

Conferring biological activity to native spider silk: A biofunctionalized protein-based microfiber.

PubMed

Wu, Hsuan-Chen; Quan, David N; Tsao, Chen-Yu; Liu, Yi; Terrell, Jessica L; Luo, Xiaolong; Yang, Jen-Chang; Payne, Gregory F; Bentley, William E

2017-01-01

Spider silk is an extraordinary material with physical properties comparable to the best scaffolding/structural materials, and as a fiber it can be manipulated with ease into a variety of configurations. Our work here demonstrates that natural spider silk fibers can also be used to organize biological components on and in devices through rapid and simple means. Micron scale spider silk fibers (5-10 μm in diameter) were surface modified with a variety of biological entities engineered with pentaglutamine tags via microbial transglutaminase (mTG). Enzymes, enzyme pathways, antibodies, and fluorescent proteins were all assembled onto spider silk fibers using this biomolecular engineering/biofabrication process. Additionally, arrangement of biofunctionalized fiber should in of itself generate a secondary level of biomolecular organization. Toward this end, as proofs of principle, spatially defined arrangement of biofunctionalized spider silk fiber was shown to generate effects specific to silk position in two cases. In one instance, arrangement perpendicular to a flow produced selective head and neck carcinoma cell capture on silk with antibodies complexed to conjugated protein G. In a second scenario, asymmetric bacterial chemotaxis arose from asymmetric conjugation of enzymes to arranged silk. Overall, the biofabrication processes used here were rapid, required no complex chemistries, were biologically benign, and also the resulting engineered silk microfibers were flexible, readily manipulated and functionally active. Deployed here in microfluidic environments, biofunctional spider silk fiber provides a means to convey complex biological functions over a range of scales, further extending its potential as a biomaterial in biotechnological settings. Biotechnol. Bioeng. 2017;114: 83-95. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Leo Szilard Lectureship Award Talk: From Reductionism to Complexity; A Theoretical Physicist's Journey into Biology and the Social Sciences

NASA Astrophysics Data System (ADS)

West, Geoffrey

2013-04-01

In this talk I review how a high energy physicist serendipitously migrated from quarks and gluons, dark matter and string theory to thinking about equally big topics like why we live for 100 years (and not a thousand or 2-3 like a mouse), how is this generated from molecular time scales, why do we sleep and where does 8 hours come from, and how is this related to the rate at which we evolve, can there be a quantitative, mathematisable science of cities and companies, and can our exponentially expanding socio-economic universe be sustained, etc, etc? I consider these as integral parts of physics, related to the interface between Reductionism and Complexity, Thermodynamics and Information Theory. The saga will be a personal one ranging from issues connected with the demise of the SSC and attacks on science to the future role of physics and transdisciplinary thinking.

Evolutionary dynamics of group interactions on structured populations: a review

PubMed Central

Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

2013-01-01

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. PMID:23303223

Shelf Sea Oxygen Dynamics: A year of Glider Measurements

NASA Astrophysics Data System (ADS)

Williams, C. A. J.; Palmer, M.; Mahaffey, C.; Jardine, J.

2016-02-01

Oxygen (O) is involved in most biogeochemical processes in the ocean, and dissolved oxygen (DO) is a well-established indicator for biological activity via the estimate of apparent oxygen utilisation (AOU). In the deep waters of the open ocean, the AOU provides a valuable insight into the ocean's biological carbon pump. However, in the physically dynamic and highly productive shallow shelf seas, interpretation of the O distribution and the magnitude of AOU is complex. Physical processes, such as diapycnal mixing, entrainment and horizontal advection act to ventilate waters below the thermocline and thus increase O and decrease AOU. In contrast, biological remineralisation of organic material below the thermocline will consume O and increase AOU. Here, we use 1 year of high-resolution data from >20 glider deployments in the seasonally stratified NW European Shelf Sea to identify and quantify the physical and biological processes that control the DO distribution and magnitude of AOU in shelf seas. A 200km transect between the shelf edge and the central Celtic Sea (CCS) was repeated between November 2014 and August 2015, thus capturing key periods in the seasonal cycling in shelf seas, specifically the onset of stratification, the spring bloom, stratified summer period and breakdown of stratification. The gliders collected data for DO, temperature, salinity, chlorophyll fluorescence, CDOM, backscatter and turbulence. In addition, direct measurements of turbulent dissipation from the Ocean Microstructure Glider deployed during the campaign provided estimates of mixing at CCS and the shelf break, allowing accurate quantification of the vertical fluxes of O. At the end of the stratified period the DO concentration was higher and AOU was lower at the shelf break (80 µM) compared to at CCS on shelf (>95 µM) (Fig 1). Estimates of vertical DO fluxes indicate that this horizontal variation in DO and AOU was partly attributed to enhanced mixing via internal waves at the shelf break ventilating waters below the thermocline, rather than decreased biological O consumption at the shelf break. Taking into consideration physical mixing processes, we provide a robust estimate of the biological O consumption over a seasonal cycle and highlight the need to consider the impact of physical processes on O dynamics in shallow shelf sea systems.

Complex Physical, Biophysical and Econophysical Systems

NASA Astrophysics Data System (ADS)

Dewar, Robert L.; Detering, Frank

1. Introduction to complex and econophysics systems: a navigation map / T. Aste and T. Di Matteo -- 2. An introduction to fractional diffusion / B. I. Henry, T.A.M. Langlands and P. Straka -- 3. Space plasmas and fusion plasmas as complex systems / R. O. Dendy -- 4. Bayesian data analysis / M. S. Wheatland -- 5. Inverse problems and complexity in earth system science / I. G. Enting -- 6. Applied fluid chaos: designing advection with periodically reoriented flows for micro to geophysical mixing and transport enhancement / G. Metcalfe -- 7. Approaches to modelling the dynamical activity of brain function based on the electroencephalogram / D. T. J. Liley and F. Frascoli -- 8. Jaynes' maximum entropy principle, Riemannian metrics and generalised least action bound / R. K. Niven and B. Andresen -- 9. Complexity, post-genomic biology and gene expression programs / R. B. H. Williams and O. J.-H. Luo -- 10. Tutorials on agent-based modelling with NetLogo and network analysis with Pajek / M. J. Berryman and S. D. Angus.

High-resolution modeling of a marine ecosystem using the FRESCO hydroecological model

NASA Astrophysics Data System (ADS)

Zalesny, V. B.; Tamsalu, R.

2009-02-01

The FRESCO (Finnish Russian Estonian Cooperation) mathematical model describing a marine hydroecosystem is presented. The methodology of the numerical solution is based on the method of multicomponent splitting into physical and biological processes, spatial coordinates, etc. The model is used for the reproduction of physical and biological processes proceeding in the Baltic Sea. Numerical experiments are performed with different spatial resolutions for four marine basins that are enclosed into one another: the Baltic Sea, the Gulf of Finland, the Tallinn-Helsinki water area, and Tallinn Bay. Physical processes are described by the equations of nonhydrostatic dynamics, including the k-ω parametrization of turbulence. Biological processes are described by the three-dimensional equations of an aquatic ecosystem with the use of a size-dependent parametrization of biochemical reactions. The main goal of this study is to illustrate the efficiency of the developed numerical technique and to demonstrate the importance of a high spatial resolution for water basins that have complex bottom topography, such as the Baltic Sea. Detailed information about the atmospheric forcing, bottom topography, and coastline is very important for the description of coastal dynamics and specific features of a marine ecosystem. Experiments show that the spatial inhomogeneity of hydroecosystem fields is caused by the combined effect of upwelling, turbulent mixing, surface-wave breaking, and temperature variations, which affect biochemical reactions.

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

Bergmann's Rule, Adaptation, and Thermoregulation in Arctic Animals: Conflicting Perspectives from Physiology, Evolutionary Biology, and Physical Anthropology After World War II.

PubMed

Hagen, Joel B

2017-05-01

Bergmann's rule and Allen's rule played important roles in mid-twentieth century discussions of adaptation, variation, and geographical distribution. Although inherited from the nineteenth-century natural history tradition these rules gained significance during the consolidation of the modern synthesis as evolutionary theorists focused attention on populations as units of evolution. For systematists, the rules provided a compelling rationale for identifying geographical races or subspecies, a function that was also picked up by some physical anthropologists. More generally, the rules provided strong evidence for adaptation by natural selection. Supporters of the rules tacitly, or often explicitly, assumed that the clines described by the rules reflected adaptations for thermoregulation. This assumption was challenged by the physiologists Laurence Irving and Per Scholander based on their arctic research conducted after World War II. Their critique spurred a controversy played out in a series of articles in Evolution, in Ernst Mayr's Animal Species and Evolution, and in the writings of other prominent evolutionary biologists and physical anthropologists. Considering this episode highlights the complexity and ambiguity of important biological concepts such as adaptation, homeostasis, and self-regulation. It also demonstrates how different disciplinary orientations and styles of scientific research influenced evolutionary explanations, and the consequent difficulties of constructing a truly synthetic evolutionary biology in the decades immediately following World War II.

The ecological risks of genetically engineered organisms

NASA Astrophysics Data System (ADS)

Wolfenbarger, Lareesa

2001-03-01

Highly publicized studies have suggested environmental risks of releasing genetically engineered organisms (GEOs) and have renewed concerns over the evaluation and regulation of these products in domestic and international arenas. I present an overview of the risks of GEOs and the available evidence addressing these and discuss the challenges for risk assessment. Main categories of risk include non-target effects from GEOs, emergence of new viral diseases, and the spread of invasive (weedy) characteristics. Studies have detected non-target effects in some cases but not all; however, much less information exists on other risks, in part due to a lack of conceptual knowledge. For example, general models for predicting invasiveness are not well developed for any introduced organism. The risks of GEOs appear comparable to those for any introduced species or organism, but the magnitude of the risk or the pathway of exposure to the risk can differ among introduced organisms. Therefore, assessing the risks requires a case-by-case analysis so that any differences can be identified. Challenges to assessing risks to valued ecosystems include variability in effects and ecosystem complexity. Ecosystems are a dynamic and complex network of biological and physical interactions. Introducing a new biological entity, such as a GEO, may potentially alter any of these interactions, but evaluating all of these is unrealistic. Effects on a valued ecosystem could vary greatly depending on the geographical location of the experimental site, the GEO used, the plot size of the experiment (scaling effects), and the biological and physical parameters used in the experiment. Experiments that address these sources of variability will provide the most useful information for risk assessments.

Evaluating Microbial Indicators of Environmental Condition in Oregon Rivers

NASA Astrophysics Data System (ADS)

Pennington, Alan T.; Harding, Anna K.; Hendricks, Charles W.; Campbell, Heidi M. K.

2001-12-01

Traditional bacterial indicators used in public health to assess water quality and the Biolog® system were evaluated to compare their response to biological, chemical, and physical habitat indicators of stream condition both within the state of Oregon and among ecoregion aggregates (Coast Range, Willamette Valley, Cascades, and eastern Oregon). Forty-three randomly selected Oregon river sites were sampled during the summer in 1997 and 1998. The public health indicators included heterotrophic plate counts (HPC), total coliforms (TC), fecal coliforms (FC) and Escherichia coli (EC). Statewide, HPC correlated strongly with physical habitat (elevation, riparian complexity, % canopy presence, and indices of agriculture, pavement, road, pasture, and total disturbance) and chemistry (pH, dissolved O2, specific conductance, acid-neutralizing capacity, dissolved organic carbon, total N, total P, SiO2, and SO4). FC and EC were significantly correlated generally with the river chemistry indicators. TC bacteria significantly correlated with riparian complexity, road disturbance, dissolved O2, and SiO2 and FC. Analyzing the sites by ecoregion, eastern Oregon was characterized by high HPC, FC, EC, nutrient loads, and indices of human disturbance, whereas the Cascades ecoregion had correspondingly low counts of these indicators. The Coast Range and Willamette Valley presented inconsistent indicator patterns that are more difficult to characterize. Attempts to distinguish between ecoregions with the Biolog system were not successful, nor did a statistical pattern emerge between the first five principle components and the other environmental indicators. Our research suggests that some traditional public health microbial indicators may be useful in measuring the environmental condition of lotic systems.

Next generation multi-scale biophysical characterization of high precision cancer particle radiotherapy using clinical proton, helium-, carbon- and oxygen ion beams

PubMed Central

Niklas, Martin; Zimmermann, Ferdinand; Chaudhri, Naved; Krunic, Damir; Tessonnier, Thomas; Ferrari, Alfredo; Parodi, Katia; Jäkel, Oliver; Debus, Jürgen; Haberer, Thomas; Abdollahi, Amir

2016-01-01

The growing number of particle therapy facilities worldwide landmarks a novel era of precision oncology. Implementation of robust biophysical readouts is urgently needed to assess the efficacy of different radiation qualities. This is the first report on biophysical evaluation of Monte Carlo simulated predictive models of prescribed dose for four particle qualities i.e., proton, helium-, carbon- or oxygen ions using raster-scanning technology and clinical therapy settings at HIT. A high level of agreement was found between the in silico simulations, the physical dosimetry and the clonogenic tumor cell survival. The cell fluorescence ion track hybrid detector (Cell-Fit-HD) technology was employed to detect particle traverse per cell nucleus. Across a panel of radiobiological surrogates studied such as late ROS accumulation and apoptosis (caspase 3/7 activation), the relative biological effectiveness (RBE) chiefly correlated with the radiation species-specific spatio-temporal pattern of DNA double strand break (DSB) formation and repair kinetic. The size and the number of residual nuclear γ-H2AX foci increased as a function of linear energy transfer (LET) and RBE, reminiscent of enhanced DNA-damage complexity and accumulation of non-repairable DSB. These data confirm the high relevance of complex DSB formation as a central determinant of cell fate and reliable biological surrogates for cell survival/RBE. The multi-scale simulation, physical and radiobiological characterization of novel clinical quality beams presented here constitutes a first step towards development of high precision biologically individualized radiotherapy. PMID:27494855

A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search

PubMed Central

Tang, Xiwei; Wang, Jianxin; Li, Min; He, Yiming; Pan, Yi

2014-01-01

Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes from the weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the weighted density, ClusterBFS detects protein complexes of the weighted network by the breadth first search algorithm, which originates from a given seed protein used as starting-point. The experimental results show that ClusterBFS performs significantly better than the other computational approaches in terms of the identification of protein complexes. PMID:24818139

Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.

PubMed

Algret, Romain; Fernandez-Martinez, Javier; Shi, Yi; Kim, Seung Joong; Pellarin, Riccardo; Cimermancic, Peter; Cochet, Emilie; Sali, Andrej; Chait, Brian T; Rout, Michael P; Dokudovskaya, Svetlana

2014-11-01

The TORC1 signaling pathway plays a major role in the control of cell growth and response to stress. Here we demonstrate that the SEA complex physically interacts with TORC1 and is an important regulator of its activity. During nitrogen starvation, deletions of SEA complex components lead to Tor1 kinase delocalization, defects in autophagy, and vacuolar fragmentation. TORC1 inactivation, via nitrogen deprivation or rapamycin treatment, changes cellular levels of SEA complex members. We used affinity purification and chemical cross-linking to generate the data for an integrative structure modeling approach, which produced a well-defined molecular architecture of the SEA complex and showed that the SEA complex comprises two regions that are structurally and functionally distinct. The SEA complex emerges as a platform that can coordinate both structural and enzymatic activities necessary for the effective functioning of the TORC1 pathway. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Functional complexity and ecosystem stability: an experimental approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Voris, P.; O'Neill, R.V.; Shugart, H.H.

1978-01-01

The complexity-stability hypothesis was experimentally tested using intact terrestrial microcosms. Functional complexity was defined as the number and significance of component interactions (i.e., population interactions, physical-chemical reactions, biological turnover rates) influenced by nonlinearities, feedbacks, and time delays. It was postulated that functional complexity could be nondestructively measured through analysis of a signal generated from the system. Power spectral analysis of hourly CO/sub 2/ efflux, from eleven old-field microcosms, was analyzed for the number of low frequency peaks and used to rank the functional complexity of each system. Ranking of ecosystem stability was based on the capacity of the system tomore » retain essential nutrients and was measured by net loss of Ca after the system was stressed. Rank correlation supported the hypothesis that increasing ecosystem functional complexity leads to increasing ecosystem stability. The results indicated that complex functional dynamics can serve to stabilize the system. The results also demonstrated that microcosms are useful tools for system-level investigations.« less

Where the girls aren't: High school girls and advanced placement physics enrollment

NASA Astrophysics Data System (ADS)

Barton, Susan O'brien

During the high school years, when many students first have some choice in course selection, research indicates that girls choose to enroll in more math and science courses, take more advanced placement courses, and take more honors courses in English, biology, chemistry, mathematics, and foreign languages than ever before. Yet, not only are boys more likely to take all of the three core science courses (biology, chemistry, and physics), boys enroll in advanced placement physics approximately three times as often as do girls. This study examines the perceptions, attitudes, and aspirations of thirty high school girls enrolled in senior-level science electives in an attempt to understand their high school science course choices, and what factors were influencing them. This is a qualitative investigation employing constructivist grounded theory methods. There are two main contributions of this study. First, it presents a new conceptual and analytical framework to investigate the problem of why some high school girls do not enroll in physics coursework. This framework is grounded in the data and is comprised of three existing feminist perspectives along the liberal/radical continuum of feminist thought. Second, this study illuminates a complex set of reasons why participants avoided high school physics (particularly advanced placement physics) coursework. These reasons emerged as three broad categories related to: (a) a lack of connectedness with physics curriculum and instruction; (b) prior negative experiences with physics and math classroom climates; and (c) future academic goals and career aspirations. Taken together, the findings of this study indicate that the problem of high school girls and physics enrollment---particularly advanced placement physics enrollment---is a problem that cannot be evaluated or considered from one perspective.

Bridging Physics and Biology Using Resistance and Axons

NASA Astrophysics Data System (ADS)

Dyer, Joshua M.

2014-11-01

When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics.1 A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite this impression held by students, there have been calls for better physics education for future physicians and life scientists.2,3 Research is being performed to improve physics classes and labs by linking topics in biology and physics.4,5 Described here is a laboratory experiment covering the topics of resistance of materials and circuits/Kirchhoff's laws in a biology context with their direct application to neurons, axons, and electrical impulse transmission within animals. This experiment will also demonstrate the mechanism believed to cause multiple sclerosis. The apparatus was designed with low-cost and readily available materials in mind.

40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Chemical, biological, and physical... FILL MATERIAL Evaluation and Testing § 230.61 Chemical, biological, and physical evaluation and testing... appropriate physical and chemical environmental characteristics. (d) Physical tests and evaluation. The effect...

The Notion of Scientific Knowledge in Biology

NASA Astrophysics Data System (ADS)

Morante, Silvia; Rossi, Giancarlo

2016-03-01

The purpose of this work is to reconsider and critically discuss the conceptual foundations of modern biology and bio-sciences in general, and provide an epistemological guideline to help framing the teaching of these disciplines and enhancing the quality of their presentation in High School, Master and Ph.D. courses. After discussing the methodological problems that arise in trying to construct a sensible and useful scientific approach applicable to the study of living systems, we illustrate what are the general requirements that a workable scheme of investigation should meet to comply with the principles of the Galilean method. The amazing success of basic physics, the Galilean science of election, can be traced back to the development of a radically " reductionistic" approach in the interpretation of experiments and a systematic procedure tailored on the paradigm of " falsifiability" aimed at consistently incorporating new information into extended models/theories. The development of bio-sciences seems to fit with neither reductionism (the deeper is the level of description of a biological phenomenon the more difficult looks finding general and simple laws), nor falsifiability (not always experiments provide a yes-or-no answer). Should we conclude that biology is not a science in the Galilean sense? We want to show that this is not so. Rather in the study of living systems, the novel interpretative paradigm of " complexity" has been developed that, without ever conflicting with the basic principles of physics, allows organizing ideas, conceiving new models and understanding the puzzling lack of reproducibility that seems to affect experiments in biology and in other modern areas of investigation. In the delicate task of conveying scientific concepts and principles to students as well as in popularising bio-sciences to a wider audience, it is of the utmost importance for the success of the process of learning to highlight the internal logical consistency of biology and its compliance with the fundamental laws of physics.

Physical modelling of the nuclear pore complex

PubMed Central

Fassati, Ariberto; Ford, Ian J.; Hoogenboom, Bart W.

2013-01-01

Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC) found perforating the nuclear envelope of eukaryotic cells. In the central conduit of the NPC, of ∼30–60 nm diameter, a disordered network of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. In spite of a wealth of experimental data, the selectivity barrier of the NPC has yet to be explained fully. Experimental and theoretical approaches are complicated by the disordered and heterogeneous nature of the NPC conduit. Modelling approaches have focused on the behaviour of the partially unfolded protein domains in the confined geometry of the NPC conduit, and have demonstrated that within the range of parameters thought relevant for the NPC, widely varying behaviour can be observed. In this review, we summarise recent efforts to physically model the NPC barrier and function. We illustrate how attempts to understand NPC barrier function have employed many different modelling techniques, each of which have contributed to our understanding of the NPC.

Treatment of ankylosing spondylitis with biologics and targeted physical therapy: positive effect on chest pain, diminished chest mobility, and respiratory function.

PubMed

Gyurcsik, Z; Bodnár, N; Szekanecz, Z; Szántó, S

2013-12-01

Biologics are highly effective in ankylosing spondylitis (AS). In this self-controlled study, we assessed the additive value of complex physiotherapy in decreasing chest pain and tenderness and improving respiratory function in AS patients treated with tumor necrosis factor α (TNF-α) inhibitors. The trial consisted of 2 parts. In study I, clinical data of AS patients with (n=55) or without biological therapy (n=20) were retrospectively analyzed and compared. Anthropometrical data, duration since diagnosis and patient assessment of disease activity, pain intensity, tender points, sacroiliac joint involvement determined by X-ray, functional condition, and physical activity level were recorded. Subjective, functional, and physical tests were performed. In study II, 10 voluntary patients (6 men and 4 women, age 52.4 ± 13.6 years) with definite AS and receiving anti-TNF therapy were recruited. It was a prospective, non-randomized physiotherapeutic trial. BASFI (Bath Ankylosing Spondylitis Functional Index), BASDAI (Bath Ankylosing Spondylitis Disease Activity Index), modified Schober Index, occiput-to-wall distance, and fingertip-to-floor distance were evaluated. Forced vital capacity, forced 1-s expiratory volume, peak expiratory flow, and maximum voluntary ventilation were recorded. Furthermore, typical tender points were recorded. A targeted physiotherapy program was conducted twice a week for 12 weeks and all above parameters were recorded at baseline and after 12 weeks. Differences in patient assessment of disease activity (p=0.019) and pain intensity (p=0.017) were found in study I. Pain and tenderness of the thoracic spine were observed in both groups. Back pain without biologic therapy was slightly higher than other group. In study II, we found that patient assessment of disease activity and pain intensity significantly improved after the physical therapy program (p=0.002 and p<0.001). BASFI and BASDAI increased after treatment (p=0.004 and p<0.001). The finger-to-floor distance, chest expansion, and modified Schober index increased (p=0.008, p<0.001, and p=0.031, respectively). The respiratory functional parameters showed a tendency towards improvement. AS patients already receiving biological therapy may benefit from additional targeted physiotherapy. Physical therapy may be of important additive value in AS patients being treated with biological. The exercise program presented here showed an improvement in functional parameters as well as spine and chest mobility, thereby enhancing the favorable effects of biological therapy.

Pectin/zein beads for potential colon-specific drug delivery: synthesis and in vitro evaluation.

PubMed

Liu, LinShu; Fishman, Marshall L; Hicks, Kevin B; Kende, Meir; Ruthel, Gordon

2006-01-01

Novel complex hydrogel beads were prepared from two edible polymers: pectin, a carbohydrate from citrus fruits, and zein, a protein from corn. The pectin/zein complex hydrogels did not swell in physiological environments, but hydrolyzed in the presence of pectinases. An in vitro study showed the capacity of the hydrogels to endure protease attack and residence time variation. The physical and biological properties of the new hydrogels were attributed to molecular entanglement of the two polymers. The pectin networks were stabilized by the bound zein molecules. In turn, the pectin networks shielded the bound zein from protease digestion.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Metal based biologically active compounds: design, synthesis, and antibacterial/antifungal/cytotoxic properties of triazole-derived Schiff bases and their oxovanadium(IV) complexes.

PubMed

Chohan, Zahid H; Sumrra, Sajjad H; Youssoufi, Moulay H; Hadda, Taibi B

2010-07-01

A new series of oxovanadium(IV) complexes have been designed and synthesized with a new class of triazole Schiff bases derived from the reaction of 3,5-diamino-1,2,4-triazole with 2-hydroxy-1-naphthaldehyde, pyrrole-2-carboxaldehyde, pyridine-2-carboxaldehyde and acetyl pyridine-2-carboxaldehyde, respectively. Physical (magnetic susceptibility, molar conductance), spectral (IR, (1)H NMR, (13)C NMR, mass and electronic) and analytical data have established the structures of these synthesized Schiff bases and their oxovanadium(IV) complexes. The Schiff bases, predominantly act as bidentate and coordinate with the vanadium(IV) metal to give a stoichiometric ratio of 1:2 [M:L], forming a general formulae, [M(L-H)(2)] and [M(L)(2)]SO(4) where L = (L(1))-(L(4)) and M = VO(IV) of these complexes in a square-pyramidal geometry. In order to evaluate the biological activity of Schiff bases and to assess the role of vanadium(IV) metal on biological activity, the triazole Schiff bases and their oxovanadium(IV) complexes have been studied for in vitro antibacterial activity against four Gram-negative (Escherichia coli, Shigella flexenari, Pseudomonas aeruginosa, Salmonella typhi) and two Gram-positive (Staphylococcus aureus, Bacillus subtilis) bacterial strains, in vitro antifungal activity against Trichophyton longifucus, Candida albican, Aspergillus flavus, Microscopum canis, Fusarium solani and Candida glaberata. The simple Schiff bases showed weaker to significant activity against one or more bacterial and fungal strains. In most of the cases higher activity was exhibited upon coordination with vanadium(IV) metal. Brine shrimp bioassay was also carried out for in vitro cytotoxic properties against Artemia salina. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Lung evolution as a cipher for physiology

PubMed Central

Torday, J. S.; Rehan, V. K.

2009-01-01

In the postgenomic era, we need an algorithm to readily translate genes into physiologic principles. The failure to advance biomedicine is due to the false hope raised in the wake of the Human Genome Project (HGP) by the promise of systems biology as a ready means of reconstructing physiology from genes. like the atom in physics, the cell, not the gene, is the smallest completely functional unit of biology. Trying to reassemble gene regulatory networks without accounting for this fundamental feature of evolution will result in a genomic atlas, but not an algorithm for functional genomics. For example, the evolution of the lung can be “deconvoluted” by applying cell-cell communication mechanisms to all aspects of lung biology development, homeostasis, and regeneration/repair. Gene regulatory networks common to these processes predict ontogeny, phylogeny, and the disease-related consequences of failed signaling. This algorithm elucidates characteristics of vertebrate physiology as a cascade of emergent and contingent cellular adaptational responses. By reducing complex physiological traits to gene regulatory networks and arranging them hierarchically in a self-organizing map, like the periodic table of elements in physics, the first principles of physiology will emerge. PMID:19366785

Synthetic transitions: towards a new synthesis

PubMed Central

Solé, Ricard

2016-01-01

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431516

Giant plasma membrane vesicles: models for understanding membrane organization.

PubMed

Levental, Kandice R; Levental, Ilya

2015-01-01

The organization of eukaryotic membranes into functional domains continues to fascinate and puzzle cell biologists and biophysicists. The lipid raft hypothesis proposes that collective lipid interactions compartmentalize the membrane into coexisting liquid domains that are central to membrane physiology. This hypothesis has proven controversial because such structures cannot be directly visualized in live cells by light microscopy. The recent observations of liquid-liquid phase separation in biological membranes are an important validation of the raft hypothesis and enable application of the experimental toolbox of membrane physics to a biologically complex phase-separated membrane. This review addresses the role of giant plasma membrane vesicles (GPMVs) in refining the raft hypothesis and expands on the application of GPMVs as an experimental model to answer some of key outstanding problems in membrane biology. Copyright © 2015 Elsevier Inc. All rights reserved.

Pattern detection in stream networks: Quantifying spatialvariability in fish distribution

USGS Publications Warehouse

Torgersen, Christian E.; Gresswell, Robert E.; Bateman, Douglas S.

2004-01-01

Biological and physical properties of rivers and streams are inherently difficult to sample and visualize at the resolution and extent necessary to detect fine-scale distributional patterns over large areas. Satellite imagery and broad-scale fish survey methods are effective for quantifying spatial variability in biological and physical variables over a range of scales in marine environments but are often too coarse in resolution to address conservation needs in inland fisheries management. We present methods for sampling and analyzing multiscale, spatially continuous patterns of stream fishes and physical habitat in small- to medium-size watersheds (500–1000 hectares). Geospatial tools, including geographic information system (GIS) software such as ArcInfo dynamic segmentation and ArcScene 3D analyst modules, were used to display complex biological and physical datasets. These tools also provided spatial referencing information (e.g. Cartesian and route-measure coordinates) necessary for conducting geostatistical analyses of spatial patterns (empirical semivariograms and wavelet analysis) in linear stream networks. Graphical depiction of fish distribution along a one-dimensional longitudinal profile and throughout the stream network (superimposed on a 10-metre digital elevation model) provided the spatial context necessary for describing and interpreting the relationship between landscape pattern and the distribution of coastal cutthroat trout (Oncorhynchus clarki clarki) in western Oregon, U.S.A. The distribution of coastal cutthroat trout was highly autocorrelated and exhibited a spherical semivariogram with a defined nugget, sill, and range. Wavelet analysis of the main-stem longitudinal profile revealed periodicity in trout distribution at three nested spatial scales corresponding ostensibly to landscape disturbances and the spacing of tributary junctions.

Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruebel, Oliver

2009-11-20

Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research coveredmore » in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle acceleration, physicists model LWFAs computationally. The datasets produced by LWFA simulations are (i) extremely large, (ii) of varying spatial and temporal resolution, (iii) heterogeneous, and (iv) high-dimensional, making analysis and knowledge discovery from complex LWFA simulation data a challenging task. To address these challenges this thesis describes the integration of the visualization system VisIt and the state-of-the-art index/query system FastBit, enabling interactive visual exploration of extremely large three-dimensional particle datasets. Researchers are especially interested in beams of high-energy particles formed during the course of a simulation. This thesis describes novel methods for automatic detection and analysis of particle beams enabling a more accurate and efficient data analysis process. By integrating these automated analysis methods with visualization, this research enables more accurate, efficient, and effective analysis of LWFA simulation data than previously possible.« less

Biological denitrification in drinking water treatment using the seaweed Gracilaria verrucosa as carbon source and biofilm carrier.

PubMed

Ovez, B; Mergaert, J; Saglam, M

2006-04-01

Chemical and microbiological aspects were investigated with regard to biological denitrification of drinking water using the seaweed Gracilaria verrucosa as the carbon and energy substrate and as physical support for the microbial flora in semibatch, fixed-bed reactors. Complete removal of nitrate (100 mg/L) was readily achieved without accumulation of nitrite. Microbiological analysis indicated that the effluent of the reactor contained high numbers of bacteria (>10(6)/mL total count). Among the 44 bacterial strains isolated directly from the samples or isolated after enrichment at 37 degrees C, 25 different fatty acid profiles were found, indicating a complex microflora, including potential pathogens.

The past, present and future of ligament regenerative engineering

PubMed Central

Mengsteab, Paulos Y; Nair, Lakshmi S; Laurencin, Cato T

2016-01-01

Regenerative engineering has been defined as the convergence of Advanced Materials Sciences, Stem Cell Sciences, Physics, Developmental Biology and Clinical Translation for the regeneration of complex tissues and organ systems. Anterior cruciate ligament (ACL) reconstruction necessitates the regeneration of bone, ligament and their interface to achieve superior clinical results. In the past, the ACL has been repaired with the use of autologous and allogeneic grafts, which have their respective drawbacks. Currently, investigations on the use of biodegradable matrices to achieve knee stability and permit tissue regeneration are making promising advancements. In the future, utilizing regenerative biology cues to induce an endogenous regenerative response may aid the enhancement of clinical ACL reconstruction outcomes. PMID:27879170

A class of traveling wave solutions for space-time fractional biological population model in mathematical physics

NASA Astrophysics Data System (ADS)

Akram, Ghazala; Batool, Fiza

2017-10-01

The (G'/G)-expansion method is utilized for a reliable treatment of space-time fractional biological population model. The method has been applied in the sense of the Jumarie's modified Riemann-Liouville derivative. Three classes of exact traveling wave solutions, hyperbolic, trigonometric and rational solutions of the associated equation are characterized with some free parameters. A generalized fractional complex transform is applied to convert the fractional equations to ordinary differential equations which subsequently resulted in number of exact solutions. It should be mentioned that the (G'/G)-expansion method is very effective and convenient for solving nonlinear partial differential equations of fractional order whose balancing number is a negative integer.

The past, present and future of ligament regenerative engineering.

PubMed

Mengsteab, Paulos Y; Nair, Lakshmi S; Laurencin, Cato T

2016-12-01

Regenerative engineering has been defined as the convergence of Advanced Materials Sciences, Stem Cell Sciences, Physics, Developmental Biology and Clinical Translation for the regeneration of complex tissues and organ systems. Anterior cruciate ligament (ACL) reconstruction necessitates the regeneration of bone, ligament and their interface to achieve superior clinical results. In the past, the ACL has been repaired with the use of autologous and allogeneic grafts, which have their respective drawbacks. Currently, investigations on the use of biodegradable matrices to achieve knee stability and permit tissue regeneration are making promising advancements. In the future, utilizing regenerative biology cues to induce an endogenous regenerative response may aid the enhancement of clinical ACL reconstruction outcomes.

Data based identification and prediction of nonlinear and complex dynamical systems

NASA Astrophysics Data System (ADS)

Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

2016-07-01

The problem of reconstructing nonlinear and complex dynamical systems from measured data or time series is central to many scientific disciplines including physical, biological, computer, and social sciences, as well as engineering and economics. The classic approach to phase-space reconstruction through the methodology of delay-coordinate embedding has been practiced for more than three decades, but the paradigm is effective mostly for low-dimensional dynamical systems. Often, the methodology yields only a topological correspondence of the original system. There are situations in various fields of science and engineering where the systems of interest are complex and high dimensional with many interacting components. A complex system typically exhibits a rich variety of collective dynamics, and it is of great interest to be able to detect, classify, understand, predict, and control the dynamics using data that are becoming increasingly accessible due to the advances of modern information technology. To accomplish these goals, especially prediction and control, an accurate reconstruction of the original system is required. Nonlinear and complex systems identification aims at inferring, from data, the mathematical equations that govern the dynamical evolution and the complex interaction patterns, or topology, among the various components of the system. With successful reconstruction of the system equations and the connecting topology, it may be possible to address challenging and significant problems such as identification of causal relations among the interacting components and detection of hidden nodes. The "inverse" problem thus presents a grand challenge, requiring new paradigms beyond the traditional delay-coordinate embedding methodology. The past fifteen years have witnessed rapid development of contemporary complex graph theory with broad applications in interdisciplinary science and engineering. The combination of graph, information, and nonlinear dynamical systems theories with tools from statistical physics, optimization, engineering control, applied mathematics, and scientific computing enables the development of a number of paradigms to address the problem of nonlinear and complex systems reconstruction. In this Review, we describe the recent advances in this forefront and rapidly evolving field, with a focus on compressive sensing based methods. In particular, compressive sensing is a paradigm developed in recent years in applied mathematics, electrical engineering, and nonlinear physics to reconstruct sparse signals using only limited data. It has broad applications ranging from image compression/reconstruction to the analysis of large-scale sensor networks, and it has become a powerful technique to obtain high-fidelity signals for applications where sufficient observations are not available. We will describe in detail how compressive sensing can be exploited to address a diverse array of problems in data based reconstruction of nonlinear and complex networked systems. The problems include identification of chaotic systems and prediction of catastrophic bifurcations, forecasting future attractors of time-varying nonlinear systems, reconstruction of complex networks with oscillatory and evolutionary game dynamics, detection of hidden nodes, identification of chaotic elements in neuronal networks, reconstruction of complex geospatial networks and nodal positioning, and reconstruction of complex spreading networks with binary data.. A number of alternative methods, such as those based on system response to external driving, synchronization, and noise-induced dynamical correlation, will also be discussed. Due to the high relevance of network reconstruction to biological sciences, a special section is devoted to a brief survey of the current methods to infer biological networks. Finally, a number of open problems including control and controllability of complex nonlinear dynamical networks are discussed. The methods outlined in this Review are principled on various concepts in complexity science and engineering such as phase transitions, bifurcations, stabilities, and robustness. The methodologies have the potential to significantly improve our ability to understand a variety of complex dynamical systems ranging from gene regulatory systems to social networks toward the ultimate goal of controlling such systems.

Climate change and occupational allergies: an overview on biological pollution, exposure and prevention.

PubMed

D'Ovidio, Maria Concetta; Annesi-Maesano, Isabella; D'Amato, Gennaro; Cecchi, Lorenzo

2016-01-01

Climate change, air pollution, temperature increase and other environmental variables are modifying air quality, contributing to the increase of prevalence of allergic respiratory diseases. Allergies are complex diseases characterized by multilevel interactions between individual susceptibility, response to immune modulation and environmental exposures to physical, chemical and biological agents. Occupational allergies introduce a further complexity to these relationships by adding occupational exposure to both the indoor and outdoor ones in the living environment. The aim of this paper is to overview climate-related allergy affecting environmental and occupational health, as literature data are scanty in this regard, and to suggest a management model of this risk based on a multidisciplinary approach, taking the case of biological pollution, with details on exposure and prevention. The management of climate-related occupational allergy should take into account preventive health strategies, environmental, public and occupational interventions, as well as to develop, implement, evaluate, and improve guidelines and standards protecting workers health under changing climatic conditions; new tools and strategies based on local conditions will have to be developed. Experimental studies and acquisition of environmental and personal data have to be matched to derive useful information for the scope of occupational health and safety.

Biology meets physics: Reductionism and multi-scale modeling of morphogenesis.

PubMed

Green, Sara; Batterman, Robert

2017-02-01

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the "tyranny of scales" problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanical modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 1: Simple VOCs and model PM

PubMed Central

Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y-H.; Jaspers, I.; Jeffries, H. E.

2013-01-01

This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity). Airborne mixtures were then created with each compound and PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA) was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and it exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells) – even if the gas-phase pollutants are not considered likely to partition to the condensed phase: the VOC-modified-PM showed significantly more damage and inflammation to lung cells than did the original PM. Because gases and PM are transported and deposited differently within the atmosphere and the lungs, these results have significant consequences. For example, current US policies for research and regulation of PM do not recognize this “effect modification” phenomena (NAS, 2004). These results present an unambiguous demonstration that – even in these simple mixtures – physical and thermal interactions alone can cause a modification of the distribution of species among the phases of airborne pollution mixtures and can result in a non-toxic phase becoming toxic due to atmospheric thermal processes only. Subsequent work extends the simple results reported here to systems with photochemical transformations of complex urban mixtures and to systems with diesel exhaust produced by different fuels. PMID:23457430

On the Concept of Information and Its Role in Nature

NASA Astrophysics Data System (ADS)

Roederer, Juan G.

2003-03-01

In this article we address some fundamental questions concerning information: Can the existing laws of physics adequately deal with the most striking property of information, namely to cause specific changes in the structure and energy flows of a complex system, without the information in itself representing fields, forces or energy in any of their characteristic forms? Or is information irreducible to the laws of physics and chemistry? Are information and complexity related concepts? Does the Universe, in its evolution, constantly generate new information? Or are information and information-processing exclusive attributes of living systems, related to the very definition of life? If that were the case, what happens with the physical meanings of entropy in statistical mechanics or wave function in quantum mechanics? How many distinct classes of information and information processing do exist in the biological world? How does information appear in Darwinian evolution? Does the human brain have unique properties or capabilities in terms of information processing? In what ways does information processing bring about human self-consciousness? We shall introduce the meaning of "information" in a way that is detached from human technological systems and related algorithms and semantics, and that is not based on any mathematical formula. To accomplish this we turn to the concept of interaction as the basic departing point, and identify two fundamentally different classes, with information and information-processing appearing as the key discriminator: force-field driven interactions between elementary particles and ensembles of particles in the macroscopic physical domain, and information-based interactions between certain kinds of complex systems that form the biological domain. We shall show that in an abiotic world, information plays no role; physical interactions just happen, they are driven by energy exchange between the interacting parts and do not require any operations of information processing. Information only enters the non-living physical world when a living thing interacts with it-and when a scientist extracts information through observation and measurement. But for living organisms, information is the very essence of their existence: to maintain a long-term state of unstable thermodynamic equilibrium with its surroundings, consistently increase its organization and reproduce, an organism has to rely on information-based interactions in which form or pattern, not energy, is the controlling factor. This latter class comprises biomolecular information processes controlling the metabolism, growth, multiplication and differentiation of cells, and neural information processes controlling animal behavior and intelligence. The only way new information can appear is through the process of biological evolution and, in the short term, through sensory acquisition and the manipulation of images in the nervous system. Non-living informational systems such as books, computers, AI systems and other artifacts, as well as living organisms that are the result of breeding or cloning, are planned by human beings and will not be considered here.

On the Advantage of Integrated Science Education in the Middle School Years

ERIC Educational Resources Information Center

Makashvili, Malkhaz; Slowinsky, Ekaterine

2009-01-01

We report on the advantage of integrating teaching of biology and physics in the 7th grade as compared to the teaching physics and biology as discrete units. Experimental group (EG) had a lesson integrating knowledge of physics and biology, while control group (CG) had discrete lessons in physics and biology, referring each to their specific…

Biological knowledge is more tentative than physics knowledge: Taiwan high school adolescents' views about the nature of biology and physics.

PubMed

Tsai, Chin-Chung

2006-01-01

Many educational psychologists believe that students' beliefs about the nature of knowledge, called epistemological beliefs, play an essential role in their learning process. Educators also stress the importance of helping students develop a better understanding of the nature of knowledge. The tentative and creative nature of science is often highlighted by contemporary science educators. However, few previous studies have investigated students' views of more specific knowledge domains, such as biology and physics. Consequently, this study developed a questionnaire to assess students' views specifically about the tentative and creative nature of biology and physics. From a survey of 428 Taiwanese high school adolescents, this study found that although students showed an understanding of the tentative and creative nature of biology and physics, they expressed stronger agreement as to the tentativeness of biology than that of physics. In addition, male students tended to agree more than did females that physics had tentative and creative features and that biology had tentative features. Also, students with more years of science education tended to show more agreement regarding the creative nature of physics and biology than those with fewer years.

Microgravity Fluids for Biology, Workshop

NASA Technical Reports Server (NTRS)

Griffin, DeVon; Kohl, Fred; Massa, Gioia D.; Motil, Brian; Parsons-Wingerter, Patricia; Quincy, Charles; Sato, Kevin; Singh, Bhim; Smith, Jeffrey D.; Wheeler, Raymond M.

2013-01-01

Microgravity Fluids for Biology represents an intersection of biology and fluid physics that present exciting research challenges to the Space Life and Physical Sciences Division. Solving and managing the transport processes and fluid mechanics in physiological and biological systems and processes are essential for future space exploration and colonization of space by humans. Adequate understanding of the underlying fluid physics and transport mechanisms will provide new, necessary insights and technologies for analyzing and designing biological systems critical to NASAs mission. To enable this mission, the fluid physics discipline needs to work to enhance the understanding of the influence of gravity on the scales and types of fluids (i.e., non-Newtonian) important to biology and life sciences. In turn, biomimetic, bio-inspired and synthetic biology applications based on physiology and biology can enrich the fluid mechanics and transport phenomena capabilities of the microgravity fluid physics community.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

NASA Astrophysics Data System (ADS)

Leiserson, Mark D. M.; Tatar, Diana; Cowen, Lenore J.; Hescott, Benjamin J.

A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome.

Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.

PubMed

Leiserson, Mark D M; Tatar, Diana; Cowen, Lenore J; Hescott, Benjamin J

2011-11-01

A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods, which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome.

Information and the Nature of Reality

NASA Astrophysics Data System (ADS)

Davies, Paul; Gregersen, Niels Henrik

2014-05-01

1. Introduction: does information matter?; Paul Davies and Niels Henrik Gregersen; Part I. History: 2. From matter to materialism and (almost) back Ernan McMullin; 3. Unsolved dilemmas: the concept of matter in the history of philosophy and in contemporary physics Philip Clayton; Part II. Physics: 4. Universe from bit Paul Davies; 5. The computational universe Seth Lloyd; 6. Minds and values in the quantum universe Henry Pierce Stapp; Part III. Biology: 7. The concept of information in biology John Maynard Smith; 8. Levels of information: Shannon-Bolzmann-Darwin Terrence W. Deacon; 9. Information and communication in living matter Bernd-Olaf Kuppers; 10. Semiotic freedom: an emerging force Jesper Hoffmeyer; 11. Care on earth: generating informed concern Holmes Rolston; Part IV. Philosophy and Theology: 12. The sciences of complexity - a new theological resource? Arthur Peacocke; 13. God as the ultimate informational principle Keith Ward; 14. Information, theology and the universe John F. Haught; 15. God, matter, and information: towards a Stoicizing Logos christology Niels Henrik Gregersen; 16. What is the 'spiritual body'? Michael Welker; Index.

Information and the Nature of Reality

NASA Astrophysics Data System (ADS)

Davies, Paul; Gregersen, Niels Henrik

2010-09-01

1. Introduction: does information matter?; Paul Davies and Niels Henrik Gregersen; Part I. History: 2. From matter to materialism and (almost) back Ernan McMullin; 3. Unsolved dilemmas: the concept of matter in the history of philosophy and in contemporary physics Philip Clayton; Part II. Physics: 4. Universe from bit Paul Davies; 5. The computational universe Seth Lloyd; 6. Minds and values in the quantum universe Henry Pierce Stapp; Part III. Biology: 7. The concept of information in biology John Maynard Smith; 8. Levels of information: Shannon-Bolzmann-Darwin Terrence W. Deacon; 9. Information and communication in living matter Bernd-Olaf Küppers; 10. Semiotic freedom: an emerging force Jesper Hoffmeyer; 11. Care on earth: generating informed concern Holmes Rolston; Part IV. Philosophy and Theology: 12. The sciences of complexity - a new theological resource? Arthur Peacocke; 13. God as the ultimate informational principle Keith Ward; 14. Information, theology and the universe John F. Haught; 15. God, matter, and information: towards a Stoicizing Logos christology Niels Henrik Gregersen; 16. What is the 'spiritual body'? Michael Welker; Index.

Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

PubMed

Panshenskov, Mikhail; Solov'yov, Ilia A; Solov'yov, Andrey V

2014-06-30

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. Copyright © 2014 Wiley Periodicals, Inc.

Physics and Biology Collaborate to Color the World

ERIC Educational Resources Information Center

Liu, Dennis W. C.

2013-01-01

To understand how life works, it is essential to understand physics and chemistry. Most biologists have a clear notion of where chemistry fits into their life sciences research and teaching. Although we are physical beings, physics does not always find a place in the biology curriculum. Physics informs and enlightens biology in myriad dimensions,…

What is biological physics?

NASA Astrophysics Data System (ADS)

Moss, Frank

1997-11-01

The question arises in a number of contexts from the editorial policies of our journals to the decisions and priorities of agencies that financially support scientific research. What kinds of papers should Physical Review E and Physical Review Letters accept within this category? What constitutes success in choosing which projects to fund? Do biological physicists discover new physics, or new biology, or do they simply make their considerable instrumental and analytical talents available to the biologists(see for example, V.A. Parsegian, Physics Today), July 1997 p. 23 and a Counterpoint by R. H. Austin, ibid p. 27.? And are there bridges to medical science? Are there now some questions in biological and medical science that cannot be creditably addressed without contemporary physics? And what does it mean that the president has ventured that the next five decades will be the age of biology as opposed to the last (which he described as the age of physics)? These questions seem interesting (at least to those who call themselves biological physicists) and may be gaining significance in view of the fact that what we loosely describe as biological physics as a field seems to be growing.

Simulations in Medicine and Biology: Insights and perspectives

NASA Astrophysics Data System (ADS)

Spyrou, George M.

2015-01-01

Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented.

Bioengineering strategies to generate artificial protein complexes.

PubMed

Kim, Heejae; Siu, Ka-Hei; Raeeszadeh-Sarmazdeh, Maryam; Sun, Qing; Chen, Qi; Chen, Wilfred

2015-08-01

For many applications, increasing synergy between distinct proteins through organization is important for the specificity, regulation, and overall reaction efficiency. Although there are many examples of protein complexes in nature, a generalized method to create these complexes remains elusive. Many conventional techniques such as random chemical conjugation, physical adsorption onto surfaces, and encapsulation within matrices are imprecise approaches and can lead to deactivation of protein native functionalities. More "bio-friendly" approaches such as genetically fused proteins and biological scaffolds often can result in low yields and low complex stability. Alternatively, site-specific protein conjugation or ligation can generate artificial protein complexes that preserve the native functionalities of protein domains and maintain stability through covalent bonds. In this review, we describe three distinct methods to synthesize artificial protein complexes (genetic incorPoration of unnatural amino acids to introduce bio-orthogonal azide and alkyne groups to proteins, split-intein based expressed protein ligation, and sortase mediated ligation) and highlight interesting applications for each technique. © 2015 Wiley Periodicals, Inc.

Report on the NASA Soft and Complex Condensed Matter Workshop

NASA Technical Reports Server (NTRS)

Singh, Bhim (Technical Monitor); Chaikin, Paul; Nagel, Sidney

2003-01-01

During the past decade, NASA has been a leading U.S. supporter of soft and complex condensed matter research. Experiments in space shuttles, MIR, the International Space Station (ISS), as well as ground-based research have provided new insights into several areas including hard sphere colloids, crystal growth, phase ordering, and transport of complex fluids at the critical point. To help define the next generation of flight experiments needed to answer remaining important questions in the field of soft and complex condensed matter, NASA's Office of Biological and Physical Science sponsored a workshop on Soft and Complex Condensed Matter, March 6, 2003. This workshop asked leading members in the field of Soft and Complex Condensed Matter (at the APS March Meeting) to help identify exciting unanswered questions in the field, along with specific research topics for which the absence of gravity would enable significant results unobtainable by other means. The workshop was attended by 24 participants from universities across the U.S. and from five different countries (in addition to NASA GRC participants).

Mosaic, self-similarity logic, and biological attraction principles: three explanatory instruments in biology.

PubMed

Agnati, Luigi F; Baluska, Frantisek; Barlow, Peter W; Guidolin, Diego

2009-11-01

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal point of view, this type of organization is the result of a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course of this 'passage through time, and suggest how today's complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely the Mosaic, Self-Similarity Logic, and the Biological Attraction principles. Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatiotemporal level under consideration. The term Mosaic indicates how, from the same set of elements assembled according to different patterns, it is possible to arrive at completely different constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction is based on the evidence that each living organism creates an attractive field around itself. This field acts as a sphere of influence that actively attracts similar fields of other biological systems, thereby modifying salient features of the interacting organisms. Three specific organizational levels of living matter, namely the molecular, cellular, and supracellular levels, have been considered in order to analyse and illustrate the interpretative as well as the predictive roles of each of these three explanatory principles.

Metals and lipid oxidation. Contemporary issues.

PubMed

Schaich, K M

1992-03-01

Lipid oxidation is now recognized to be a critically important reaction in physiological and toxicological processes as well as in food products. This provides compelling reasons to understand what causes lipid oxidation in order to be able to prevent or control the reactions. Redox-active metals are major factors catalyzing lipid oxidation in biological systems. Classical mechanisms of direct electron transfer to double bonds by higher valence metals and of reduction of hydroperoxides by lower valence metals do not always account for patterns of metal catalysis of lipid oxidation in multiphasic or compartmentalized biological systems. To explain why oxidation kinetics, mechanisms, and products in molecular environments which are both chemically and physically complex often do not follow classical patterns predicted by model system studies, increased consideration must be given to five contemporary issues regarding metal catalysis of lipid oxidation: hypervalent non-heme iron or iron-oxygen complexes, heme catalysis mechanism(s), compartmentalization of reactions and lipid phase reactions of metals, effects of metals on product mixes, and factors affecting the mode of metal catalytic action.

Tensegrity II. How structural networks influence cellular information processing networks

NASA Technical Reports Server (NTRS)

Ingber, Donald E.

2003-01-01

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Computational oncology.

PubMed

Lefor, Alan T

2011-08-01

Oncology research has traditionally been conducted using techniques from the biological sciences. The new field of computational oncology has forged a new relationship between the physical sciences and oncology to further advance research. By applying physics and mathematics to oncologic problems, new insights will emerge into the pathogenesis and treatment of malignancies. One major area of investigation in computational oncology centers around the acquisition and analysis of data, using improved computing hardware and software. Large databases of cellular pathways are being analyzed to understand the interrelationship among complex biological processes. Computer-aided detection is being applied to the analysis of routine imaging data including mammography and chest imaging to improve the accuracy and detection rate for population screening. The second major area of investigation uses computers to construct sophisticated mathematical models of individual cancer cells as well as larger systems using partial differential equations. These models are further refined with clinically available information to more accurately reflect living systems. One of the major obstacles in the partnership between physical scientists and the oncology community is communications. Standard ways to convey information must be developed. Future progress in computational oncology will depend on close collaboration between clinicians and investigators to further the understanding of cancer using these new approaches.

The Mediating Role of Physical Self-Concept on Relations between Biological Maturity Status and Physical Activity in Adolescent Females

ERIC Educational Resources Information Center

Cumming, Sean P.; Standage, Martyn; Loney, Tom; Gammon, Catherine; Neville, Helen; Sherar, Lauren B.; Malina, Robert M.

2011-01-01

The current study examined the mediating role of physical self-concept on relations between biological maturity status and self-reported physical activity in adolescent British females. Biological maturity status, physical self-concept and physical activity were assessed in 407 female British year 7-9 pupils (M age = 13.2 years, SD = 1.0).…

An instructional design process based on expert knowledge for teaching students how mechanisms are explained.

PubMed

Trujillo, Caleb M; Anderson, Trevor R; Pelaez, Nancy J

2016-06-01

In biology and physiology courses, students face many difficulties when learning to explain mechanisms, a topic that is demanding due to the immense complexity and abstract nature of molecular and cellular mechanisms. To overcome these difficulties, we asked the following question: how does an instructor transform their understanding of biological mechanisms and other difficult-to-learn topics so that students can comprehend them? To address this question, we first reviewed a model of the components used by biologists to explain molecular and cellular mechanisms: the MACH model, with the components of methods (M), analogies (A), context (C), and how (H). Next, instructional materials were developed and the teaching activities were piloted with a physical MACH model. Students who used the MACH model to guide their explanations of mechanisms exhibited both improvements and some new difficulties. Third, a series of design-based research cycles was applied to bring the activities with an improved physical MACH model into biology and biochemistry courses. Finally, a useful rubric was developed to address prevalent student difficulties. Here, we present, for physiology and biology instructors, the knowledge and resources for explaining molecular and cellular mechanisms in undergraduate courses with an instructional design process aimed at realizing pedagogical content knowledge for teaching. Our four-stage process could be adapted to advance instruction with a range of models in the life sciences. Copyright © 2016 The American Physiological Society.

An instructional design process based on expert knowledge for teaching students how mechanisms are explained

PubMed Central

Anderson, Trevor R.; Pelaez, Nancy J.

2016-01-01

In biology and physiology courses, students face many difficulties when learning to explain mechanisms, a topic that is demanding due to the immense complexity and abstract nature of molecular and cellular mechanisms. To overcome these difficulties, we asked the following question: how does an instructor transform their understanding of biological mechanisms and other difficult-to-learn topics so that students can comprehend them? To address this question, we first reviewed a model of the components used by biologists to explain molecular and cellular mechanisms: the MACH model, with the components of methods (M), analogies (A), context (C), and how (H). Next, instructional materials were developed and the teaching activities were piloted with a physical MACH model. Students who used the MACH model to guide their explanations of mechanisms exhibited both improvements and some new difficulties. Third, a series of design-based research cycles was applied to bring the activities with an improved physical MACH model into biology and biochemistry courses. Finally, a useful rubric was developed to address prevalent student difficulties. Here, we present, for physiology and biology instructors, the knowledge and resources for explaining molecular and cellular mechanisms in undergraduate courses with an instructional design process aimed at realizing pedagogical content knowledge for teaching. Our four-stage process could be adapted to advance instruction with a range of models in the life sciences. PMID:27231262

40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Chemical, biological, and physical... FILL MATERIAL Evaluation and Testing § 230.61 Chemical, biological, and physical evaluation and testing... approaches or procedures will be furnished by the permitting authority. (b) Chemical-biological interactive...

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins.

PubMed

Uversky, Vladimir N

2016-03-25

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks

PubMed Central

Krüger, Antje; Csibra, Eszter; Gianni, Edoardo

2016-01-01

Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs. PMID:27903826

Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks

NASA Astrophysics Data System (ADS)

Mehta, Pankaj; Lang, Alex H.; Schwab, David J.

2016-03-01

A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to understand and manipulate cellular information processing networks raises several fundamental physics questions: How do the molecular components of cellular circuits exploit energy consumption to improve information processing? Can one utilize ideas from thermodynamics to improve the design of synthetic cellular circuits and modules? Here, we summarize recent theoretical work addressing these questions. Energy consumption in cellular circuits serves five basic purposes: (1) increasing specificity, (2) manipulating dynamics, (3) reducing variability, (4) amplifying signal, and (5) erasing memory. We demonstrate these ideas using several simple examples and discuss the implications of these theoretical ideas for the emerging field of synthetic biology. We conclude by discussing how it may be possible to overcome these limitations using "post-translational" synthetic biology that exploits reversible protein modification.

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks.

PubMed

Torres, Leticia; Krüger, Antje; Csibra, Eszter; Gianni, Edoardo; Pinheiro, Vitor B

2016-11-30

Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs. © 2016 The Author(s).

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

DOE PAGES

Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.; ...

2017-04-12

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

Rich complex behaviour of self-assembled nanoparticles far from equilibrium

PubMed Central

Ilday, Serim; Makey, Ghaith; Akguc, Gursoy B.; Yavuz, Özgün; Tokel, Onur; Pavlov, Ihor; Gülseren, Oguz; Ilday, F. Ömer

2017-01-01

A profoundly fundamental question at the interface between physics and biology remains open: what are the minimum requirements for emergence of complex behaviour from nonliving systems? Here, we address this question and report complex behaviour of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: the system is driven far from equilibrium by ultrafast laser pulses that create spatiotemporal temperature gradients, inducing Marangoni flow that drags particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation. Nonlinear feedback mechanisms naturally arise between flow, aggregate and Brownian motion, allowing fast external control with minimal intervention. Consequently, complex behaviour, analogous to those seen in living organisms, emerges, whereby aggregates can self-sustain, self-regulate, self-replicate, self-heal and can be transferred from one location to another, all within seconds. Aggregates can comprise only one pattern or bifurcated patterns can coexist, compete, endure or perish. PMID:28443636

Rich complex behaviour of self-assembled nanoparticles far from equilibrium

NASA Astrophysics Data System (ADS)

Ilday, Serim; Makey, Ghaith; Akguc, Gursoy B.; Yavuz, Özgün; Tokel, Onur; Pavlov, Ihor; Gülseren, Oguz; Ilday, F. Ömer

2017-04-01

A profoundly fundamental question at the interface between physics and biology remains open: what are the minimum requirements for emergence of complex behaviour from nonliving systems? Here, we address this question and report complex behaviour of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: the system is driven far from equilibrium by ultrafast laser pulses that create spatiotemporal temperature gradients, inducing Marangoni flow that drags particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation. Nonlinear feedback mechanisms naturally arise between flow, aggregate and Brownian motion, allowing fast external control with minimal intervention. Consequently, complex behaviour, analogous to those seen in living organisms, emerges, whereby aggregates can self-sustain, self-regulate, self-replicate, self-heal and can be transferred from one location to another, all within seconds. Aggregates can comprise only one pattern or bifurcated patterns can coexist, compete, endure or perish.

Extending Quantum Chemistry of Bound States to Electronic Resonances

NASA Astrophysics Data System (ADS)

Jagau, Thomas-C.; Bravaya, Ksenia B.; Krylov, Anna I.

2017-05-01

Electronic resonances are metastable states with finite lifetime embedded in the ionization or detachment continuum. They are ubiquitous in chemistry, physics, and biology. Resonances play a central role in processes as diverse as DNA radiolysis, plasmonic catalysis, and attosecond spectroscopy. This review describes novel equation-of-motion coupled-cluster (EOM-CC) methods designed to treat resonances and bound states on an equal footing. Built on complex-variable techniques such as complex scaling and complex absorbing potentials that allow resonances to be associated with a single eigenstate of the molecular Hamiltonian rather than several continuum eigenstates, these methods extend electronic-structure tools developed for bound states to electronic resonances. Selected examples emphasize the formal advantages as well as the numerical accuracy of EOM-CC in the treatment of electronic resonances. Connections to experimental observables such as spectra and cross sections, as well as practical aspects of implementing complex-valued approaches, are also discussed.

Dual-phase evolution in complex adaptive systems

PubMed Central

Paperin, Greg; Green, David G.; Sadedin, Suzanne

2011-01-01

Understanding the origins of complexity is a key challenge in many sciences. Although networks are known to underlie most systems, showing how they contribute to well-known phenomena remains an issue. Here, we show that recurrent phase transitions in network connectivity underlie emergent phenomena in many systems. We identify properties that are typical of systems in different connectivity phases, as well as characteristics commonly associated with the phase transitions. We synthesize these common features into a common framework, which we term dual-phase evolution (DPE). Using this framework, we review the literature from several disciplines to show that recurrent connectivity phase transitions underlie the complex properties of many biological, physical and human systems. We argue that the DPE framework helps to explain many complex phenomena, including perpetual novelty, modularity, scale-free networks and criticality. Our review concludes with a discussion of the way DPE relates to other frameworks, in particular, self-organized criticality and the adaptive cycle. PMID:21247947

Dual-phase evolution in complex adaptive systems.

PubMed

Paperin, Greg; Green, David G; Sadedin, Suzanne

2011-05-06

Understanding the origins of complexity is a key challenge in many sciences. Although networks are known to underlie most systems, showing how they contribute to well-known phenomena remains an issue. Here, we show that recurrent phase transitions in network connectivity underlie emergent phenomena in many systems. We identify properties that are typical of systems in different connectivity phases, as well as characteristics commonly associated with the phase transitions. We synthesize these common features into a common framework, which we term dual-phase evolution (DPE). Using this framework, we review the literature from several disciplines to show that recurrent connectivity phase transitions underlie the complex properties of many biological, physical and human systems. We argue that the DPE framework helps to explain many complex phenomena, including perpetual novelty, modularity, scale-free networks and criticality. Our review concludes with a discussion of the way DPE relates to other frameworks, in particular, self-organized criticality and the adaptive cycle.

Evolution of an ancient protein function involved in organized multicellularity in animals.

PubMed

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-07

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which - the evolution of GKPID's capacity to bind the cortical marker protein - can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.

Energy deposition processes in biological tissue: nonthermal biohazards seem unlikely in the ultra-high frequency range.

PubMed

Pickard, W F; Moros, E G

2001-02-01

The prospects of ultra high frequency (UHF, 300--3000 MHz) irradiation producing a nonthermal bioeffect are considered theoretically and found to be small. First, a general formula is derived within the framework of macroscopic electrodynamics for the specific absorption rate of microwaves in a biological tissue; this involves the complex Poynting vector, the mass density of the medium, the angular frequency of the electromagnetic field, and the three complex electromagnetic constitutive parameters of the medium. In the frequency ranges used for cellular telephony and personal communication systems, this model predicts that the chief physical loss mechanism will be ionic conduction, with increasingly important contributions from dielectric relaxation as the frequency rises. However, even in a magnetite unit cell within a magnetosome the deposition rate should not exceed 1/10 k(B)T per second. This supports previous arguments for the improbability of biological effects at UHF frequencies unless a mechanism can be found for accumulating energy over time and space and focussing it. Second, three possible nonthermal accumulation mechanisms are then considered and shown to be unlikely: (i) multiphoton absorption processes; (ii) direct electric field effects on ions; (iii) cooperative effects and/or coherent excitations. Finally, it is concluded that the rate of energy deposition from a typical field and within a typical tissue is so small as to make unlikely any significant nonthermal biological effect. Copyright 2001 Wiley-Liss, Inc.

Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol

PubMed Central

Prather, Kimberly A.; Bertram, Timothy H.; Grassian, Vicki H.; Deane, Grant B.; Stokes, M. Dale; DeMott, Paul J.; Aluwihare, Lihini I.; Palenik, Brian P.; Azam, Farooq; Seinfeld, John H.; Moffet, Ryan C.; Molina, Mario J.; Cappa, Christopher D.; Geiger, Franz M.; Roberts, Gregory C.; Russell, Lynn M.; Ault, Andrew P.; Baltrusaitis, Jonas; Collins, Douglas B.; Corrigan, Craig E.; Cuadra-Rodriguez, Luis A.; Ebben, Carlena J.; Forestieri, Sara D.; Guasco, Timothy L.; Hersey, Scott P.; Kim, Michelle J.; Lambert, William F.; Modini, Robin L.; Mui, Wilton; Pedler, Byron E.; Ruppel, Matthew J.; Ryder, Olivia S.; Schoepp, Nathan G.; Sullivan, Ryan C.; Zhao, Defeng

2013-01-01

The production, size, and chemical composition of sea spray aerosol (SSA) particles strongly depend on seawater chemistry, which is controlled by physical, chemical, and biological processes. Despite decades of studies in marine environments, a direct relationship has yet to be established between ocean biology and the physicochemical properties of SSA. The ability to establish such relationships is hindered by the fact that SSA measurements are typically dominated by overwhelming background aerosol concentrations even in remote marine environments. Herein, we describe a newly developed approach for reproducing the chemical complexity of SSA in a laboratory setting, comprising a unique ocean-atmosphere facility equipped with actual breaking waves. A mesocosm experiment was performed in natural seawater, using controlled phytoplankton and heterotrophic bacteria concentrations, which showed SSA size and chemical mixing state are acutely sensitive to the aerosol production mechanism, as well as to the type of biological species present. The largest reduction in the hygroscopicity of SSA occurred as heterotrophic bacteria concentrations increased, whereas phytoplankton and chlorophyll-a concentrations decreased, directly corresponding to a change in mixing state in the smallest (60–180 nm) size range. Using this newly developed approach to generate realistic SSA, systematic studies can now be performed to advance our fundamental understanding of the impact of ocean biology on SSA chemical mixing state, heterogeneous reactivity, and the resulting climate-relevant properties. PMID:23620519

Infrastructure Tsunami Could Easily Dwarf Climate Change

NASA Astrophysics Data System (ADS)

Lansing, Stephen

Compared to the physical and biological sciences, so far complexity has had far less impact on mainstream social science. This is not surprising, but it is alarming because we find ourselves in the midst of a planetary-scale transition from the Holocene to the Anthropocene. We have already breached some planetary boundaries for sustainability, but those tipping points are nearly invisible from the perspective of the linear equilibrium models that continue to hold sway in social science...

Differential Multiscale Modeling of Chemically Complex Materials under Heavy Deformation: Biological, Bioinspired and Synthetic Hierarchical Materials

DTIC Science & Technology

2010-06-01

Buehler, “Meso- Origami : Folding Multilayer Graphene Sheets”, Applied Physics Letters, Vol. 95, paper #: 123121, 2009 D. Sen and M.J. Buehler, “Size and... geometry effects on flow stress in bioinspired de novo metal-matrix nanocomposites”, Advanced Engineering Materials, Vol. 11(10), pp. 774-781, 2009...behavior is recovered. Second, a subset of all geometries shows the inverse banana curve behavior. Interestingly, only 2% of all structures give the

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cranbrook, The Earl of.

After a century of scientific investigation, it is now possible to understand Malaysia's complex ecosystem as an essential prerequisite to the successful management for conservation and long term productivity in the area. Contents: The physical setting: Forest types and forest zonation; The dipterocarps; Forest palms; Forest bamboos; Herbaceous flowering plants; Ferns; Higher fungi; Forest tree biology; Forest management; Mammals; Genetic diversity and evolution; Mammals; Distribution and ecology, Earl of Cranbook, Birds; Termites in rain forests; Forest lepidoptera; Freshwaters; Animal conservation strategies; People of the forest.

Emerging new strategies for successful metabolite identification in metabolomics

PubMed Central

Bingol, Kerem; Bruschweiler-Li, Lei; Li, Dawei; Zhang, Bo; Xie, Mouzhe; Brüschweiler, Rafael

2016-01-01

This review discusses strategies for the identification of metabolites in complex biological mixtures, as encountered in metabolomics, which have emerged in the recent past. These include NMR database-assisted approaches for the identification of commonly known metabolites as well as novel combinations of NMR and MS analysis methods for the identification of unknown metabolites. The use of certain chemical additives to the NMR tube can permit identification of metabolites with specific physical chemical properties. PMID:26915807

Geophysical fluid dynamics: whence, whither and why?

PubMed Central

2016-01-01

This article discusses the role of geophysical fluid dynamics (GFD) in understanding the natural environment, and in particular the dynamics of atmospheres and oceans on Earth and elsewhere. GFD, as usually understood, is a branch of the geosciences that deals with fluid dynamics and that, by tradition, seeks to extract the bare essence of a phenomenon, omitting detail where possible. The geosciences in general deal with complex interacting systems and in some ways resemble condensed matter physics or aspects of biology, where we seek explanations of phenomena at a higher level than simply directly calculating the interactions of all the constituent parts. That is, we try to develop theories or make simple models of the behaviour of the system as a whole. However, these days in many geophysical systems of interest, we can also obtain information for how the system behaves by almost direct numerical simulation from the governing equations. The numerical model itself then explicitly predicts the emergent phenomena—the Gulf Stream, for example—something that is still usually impossible in biology or condensed matter physics. Such simulations, as manifested, for example, in complicated general circulation models, have in some ways been extremely successful and one may reasonably now ask whether understanding a complex geophysical system is necessary for predicting it. In what follows we discuss such issues and the roles that GFD has played in the past and will play in the future. PMID:27616918

PREFACE: 1st-2nd Young Researchers Meetings in Rome - Proceedings

NASA Astrophysics Data System (ADS)

YRMR Organizing Committee; Cannuccia, E.; Mazzaferro, L.; Migliaccio, M.; Pietrobon, D.; Stellato, F.; Veneziani, M.

2011-03-01

Students in science, particularly in physics, face a fascinating and challenging future. Scientists have proposed very interesting theories, which describe the microscopic and macroscopic world fairly well, trying to match the quantum regime with cosmological scales. Between the extremes of this scenario, biological phenomena in all their complexity take place, challenging the laws we observe in the atomic and sub-atomic world. More and more accurate and complex experiments have been devised and these are now going to test the paradigms of physics. Notable experiments include: the Large Hadronic Collider (LHC), which is going to shed light on the physics of the Standard Model of Particles and its extensions; the Planck-Herschel satellites, which target a very precise measurement of the properties of our Universe; and the Free Electron Lasers facilities, which produce high-brilliance, ultrafast X-ray pulses, allowing the investigation of the fundamental processes of solid state physics, chemistry, and biology. These projects are the result of huge collaborations spread across the world, involving scientists belonging to different and complementary research fields: physicists, chemists, biologists and others, keen to make the best of these extraordinary laboratories. Even though each branch of science is experiencing a process of growing specialization, it is very important to keep an eye on the global picture, remaining aware of the deep interconnections between inherent fields. This is even more crucial for students who are beginning their research careers. These considerations motivated PhD students and young post-docs connected to the Roman scientific research area to organize a conference, to establish the background and the network for interactions and collaborations. This resulted in the 1st and 2nd Young Researchers Meetings in Rome (http://ryrm.roma2.infn.it), one day conferences aimed primarily at graduate students and post-docs, working in physics in Italy and abroad. In its first two editions, the meeting was held at the Universities of Roma "Tor Vergata" (July 2009) and "LaSapienza" (February 2010), and organized in sections dedicated to up-to-date topics spanning broad research fields: Astrophysics-Cosmology, Soft-Condensed Matter Physics, Theoretical-Particle Physics, and Medical Physics. In these proceedings we have collected some of the contributions which were presented during the meetings.

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

Fitting in or opting out: A review of key social-psychological factors influencing a sense of belonging for women in physics

NASA Astrophysics Data System (ADS)

Lewis, Karyn L.; Stout, Jane G.; Pollock, Steven J.; Finkelstein, Noah D.; Ito, Tiffany A.

2016-12-01

[This paper is part of the Focused Collection on Gender in Physics.] A number of cultural, social, environmental, and biological factors have been suggested to explain women's relatively lower representation in physics and other science, technology, engineering, and math (STEM) fields. Given its persistence, the causes of gender disparities are likely to be complex and multiply determined. In this review paper, we discuss how a sense of belonging relates to women's interest, persistence, and achievement in physics. We explore what it means to "fit in" and belong in academic contexts, the situational and interpersonal antecedents to belonging, and the consequences of a lack of belonging. We review the empirical evidence for the efficacy of interventions designed to bolster a sense of belonging. Based on these interventions we conclude the paper with a number of practical recommendations to affirm women's sense of belonging and create more welcoming and inclusive physics environments for all students.

Biological consequences of nanoscale energy deposition near irradiated heavy atom nanoparticles

PubMed Central

McMahon, Stephen J.; Hyland, Wendy B.; Muir, Mark F.; Coulter, Jonathan A.; Jain, Suneil; Butterworth, Karl T.; Schettino, Giuseppe; Dickson, Glenn R.; Hounsell, Alan R.; O'Sullivan, Joe M.; Prise, Kevin M.; Hirst, David G.; Currell, Fred J.

2011-01-01

Gold nanoparticles (GNPs) are being proposed as contrast agents to enhance X-ray imaging and radiotherapy, seeking to take advantage of the increased X-ray absorption of gold compared to soft tissue. However, there is a great discrepancy between physically predicted increases in X-ray energy deposition and experimentally observed increases in cell killing. In this work, we present the first calculations which take into account the structure of energy deposition in the nanoscale vicinity of GNPs and relate this to biological outcomes, and show for the first time good agreement with experimentally observed cell killing by the combination of X-rays and GNPs. These results are not only relevant to radiotherapy, but also have implications for applications of heavy atom nanoparticles in biological settings or where human exposure is possible because the localised energy deposition high-lighted by these results may cause complex DNA damage, leading to mutation and carcinogenesis. PMID:22355537

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins*

PubMed Central

2016-01-01

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. PMID:26851286

Fluorescence dynamics of biological systems using synchrotron radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gratton, E.; Mantulin, W.W.; Weber, G.

1996-09-01

A beamline for time-resolved fluorescence spectroscopy of biological systems is under construction at the Synchrotron Radiation Center. The fluorometer, operating in the frequency domain, will take advantage of the time structure of the synchrotron radiation light pulses to determine fluorescence lifetimes. Using frequency-domain techniques, the instrument can achieve an ultimate time resolution on the order of picoseconds. Preliminary experiments have shown that reducing the intensity of one of the fifteen electron bunches in the storage ring allows measurement of harmonic frequencies equivalent to the single-bunch mode. This mode of operation of the synchrotron significantly extends the range of lifetimes thatmore » can be measured. The wavelength range (encompassing the visible and ultraviolet), the range of measurable lifetimes, and the stability and reproducibility of the storage ring pulses should make this beamline a versatile tool for the investigation of the complex fluorescence decay of biological systems. {copyright} {ital 1996 American Institute of Physics.}« less

Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe.

PubMed

Moore, Jeremiah D; Lord, Richard L; Cisneros, G Andrés; Allen, Matthew J

2012-10-24

A pH-responsive, luminescent, dimetallic Eu(III)-containing complex has been synthesized and exhibits a unique mechanism of response. The luminescence-decay rate of the complex is slow, due to a lack of water molecules coordinated to the Eu(III) ions. However, the luminescence-decay rate decreases with increasing pH over a biologically relevant range of 4-8. Physical characterization and computational analysis suggest that the pH response is due to protonation of a bridging alkoxide at lower pH values. Modulation of the luminescence-decay rate is independent from the concentration of Eu(III), which we expect to be useful in the non-invasive imaging of in vivo pH.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

PubMed Central

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

Varieties of noise: analogical reasoning in synthetic biology.

PubMed

Knuuttila, Tarja; Loettgers, Andrea

2014-12-01

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

The physics of epigenetics

NASA Astrophysics Data System (ADS)

Cortini, Ruggero; Barbi, Maria; Caré, Bertrand R.; Lavelle, Christophe; Lesne, Annick; Mozziconacci, Julien; Victor, Jean-Marc

2016-04-01

In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics: the stable and inheritable changes in gene expression patterns. This article reviews the extremely rich and exquisitely multiscale physical mechanisms that govern the biological processes behind the initiation, spreading, and inheritance of epigenetic states. These include not only the changes in the molecular properties associated with the chemical modifications of DNA and histone proteins, such as methylation and acetylation, but also less conventional changes, typically in the physics that governs the three-dimensional organization of the genome in cell nuclei. Strikingly, to achieve stability and heritability of epigenetic states, cells take advantage of many different physical principles, such as the universal behavior of polymers and copolymers, the general features of dynamical systems, and the electrostatic and mechanical properties related to chemical modifications of DNA and histones. By putting the complex biological literature in this new light, the emerging picture is that a limited set of general physical rules play a key role in initiating, shaping, and transmitting this crucial "epigenetic landscape." This new perspective not only allows one to rationalize the normal cellular functions, but also helps to understand the emergence of pathological states, in which the epigenetic landscape becomes dysfunctional.

The Physical Microbe; An introduction to noise, control, and communication in the prokaryotic cell

NASA Astrophysics Data System (ADS)

Hagen, Stephen J.

2017-10-01

Physical biology is a fusion of biology and physics. This book narrows down the scope of physical biology by focusing on the microbial cell; exploring the physical phenomena of noise, feedback, and variability that arise in the cellular information-processing circuits used by bacteria. It looks at the microbe from a physics perspective, asking how the cell optimizes its function to live within the constraints of physics. It introduces a physical and information-based (as opposed to microbiological) perspective on communication and signalling between microbes.

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

PubMed

Schäfer, Bernhard; Greisch, Jean-François; Faus, Isabelle; Bodenstein, Tilmann; Šalitroš, Ivan; Fuhr, Olaf; Fink, Karin; Schünemann, Volker; Kappes, Manfred M; Ruben, Mario

2016-08-26

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Large eddy simulation modeling of particle-laden flows in complex terrain

NASA Astrophysics Data System (ADS)

Salesky, S.; Giometto, M. G.; Chamecki, M.; Lehning, M.; Parlange, M. B.

2017-12-01

The transport, deposition, and erosion of heavy particles over complex terrain in the atmospheric boundary layer is an important process for hydrology, air quality forecasting, biology, and geomorphology. However, in situ observations can be challenging in complex terrain due to spatial heterogeneity. Furthermore, there is a need to develop numerical tools that can accurately represent the physics of these multiphase flows over complex surfaces. We present a new numerical approach to accurately model the transport and deposition of heavy particles in complex terrain using large eddy simulation (LES). Particle transport is represented through solution of the advection-diffusion equation including terms that represent gravitational settling and inertia. The particle conservation equation is discretized in a cut-cell finite volume framework in order to accurately enforce mass conservation. Simulation results will be validated with experimental data, and numerical considerations required to enforce boundary conditions at the surface will be discussed. Applications will be presented in the context of snow deposition and transport, as well as urban dispersion.

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

PubMed Central

Leiserson, Mark D.M.; Tatar, Diana; Cowen, Lenore J.

2011-01-01

Abstract A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods, which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome. PMID:21882903

Role of Tai Chi in the treatment of rheumatologic diseases.

PubMed

Wang, Chenchen

2012-12-01

Rheumatologic diseases (e.g., fibromyalgia, osteoarthritis, and rheumatoid arthritis) consist of a complex interplay between biologic and psychological aspects, resulting in therapeutically challenging chronic conditions to control. Encouraging evidence suggests that Tai Chi, a multi-component Chinese mind-body exercise, has multiple benefits for patients with a variety of chronic disorders, particularly those with musculoskeletal conditions. Thus, Tai Chi may modulate complex factors and improve health outcomes in patients with chronic rheumatologic conditions. As a form of physical exercise, Tai Chi enhances cardiovascular fitness, muscular strength, balance, and physical function. It also appears to be associated with reduced stress, anxiety, and depression, as well as improved quality of life. Thus, Tai Chi can be safely recommended to patients with fibromyalgia, osteoarthritis, and rheumatoid arthritis as a complementary and alternative medical approach to improve patient well-being. This review highlights the current body of knowledge about the role of this ancient Chinese mind-body medicine as an effective treatment of rheumatologic diseases to better inform clinical decision-making for our patients.

Real-time full-field characterization of transient dissipative soliton dynamics in a mode-locked laser

NASA Astrophysics Data System (ADS)

Ryczkowski, P.; Närhi, M.; Billet, C.; Merolla, J.-M.; Genty, G.; Dudley, J. M.

2018-04-01

Dissipative solitons are remarkably localized states of a physical system that arise from the dynamical balance between nonlinearity, dispersion and environmental energy exchange. They are the most universal form of soliton that can exist, and are seen in far-from-equilibrium systems in many fields, including chemistry, biology and physics. There has been particular interest in studying their properties in mode-locked lasers, but experiments have been limited by the inability to track the dynamical soliton evolution in real time. Here, we use simultaneous dispersive Fourier transform and time-lens measurements to completely characterize the spectral and temporal evolution of ultrashort dissipative solitons as their dynamics pass through a transient unstable regime with complex break-up and collisions before stabilization. Further insight is obtained from reconstruction of the soliton amplitude and phase and calculation of the corresponding complex-valued eigenvalue spectrum. These findings show how real-time measurements provide new insights into ultrafast transient dynamics in optics.

Migration of cells in a social context

PubMed Central

Vedel, Søren; Tay, Savaş; Johnston, Darius M.; Bruus, Henrik; Quake, Stephen R.

2013-01-01

In multicellular organisms and complex ecosystems, cells migrate in a social context. Whereas this is essential for the basic processes of life, the influence of neighboring cells on the individual remains poorly understood. Previous work on isolated cells has observed a stereotypical migratory behavior characterized by short-time directional persistence with long-time random movement. We discovered a much richer dynamic in the social context, with significant variations in directionality, displacement, and speed, which are all modulated by local cell density. We developed a mathematical model based on the experimentally identified “cellular traffic rules” and basic physics that revealed that these emergent behaviors are caused by the interplay of single-cell properties and intercellular interactions, the latter being dominated by a pseudopod formation bias mediated by secreted chemicals and pseudopod collapse following collisions. The model demonstrates how aspects of complex biology can be explained by simple rules of physics and constitutes a rapid test bed for future studies of collective migration of individual cells. PMID:23251032

Migration of cells in a social context.

PubMed

Vedel, Søren; Tay, Savaş; Johnston, Darius M; Bruus, Henrik; Quake, Stephen R

2013-01-02

In multicellular organisms and complex ecosystems, cells migrate in a social context. Whereas this is essential for the basic processes of life, the influence of neighboring cells on the individual remains poorly understood. Previous work on isolated cells has observed a stereotypical migratory behavior characterized by short-time directional persistence with long-time random movement. We discovered a much richer dynamic in the social context, with significant variations in directionality, displacement, and speed, which are all modulated by local cell density. We developed a mathematical model based on the experimentally identified "cellular traffic rules" and basic physics that revealed that these emergent behaviors are caused by the interplay of single-cell properties and intercellular interactions, the latter being dominated by a pseudopod formation bias mediated by secreted chemicals and pseudopod collapse following collisions. The model demonstrates how aspects of complex biology can be explained by simple rules of physics and constitutes a rapid test bed for future studies of collective migration of individual cells.

A supramolecular complex between proteinases and beta-cyclodextrin that preserves enzymatic activity: physicochemical characterization.

PubMed

Denadai, Angelo M L; Santoro, Marcelo M; Lopes, Miriam T P; Chenna, Angélica; de Sousa, Frederico B; Avelar, Gabriela M; Gomes, Marco R Túlio; Guzman, Fanny; Salas, Carlos E; Sinisterra, Rubén D

2006-01-01

Cyclodextrins are suitable drug delivery systems because of their ability to subtly modify the physical, chemical, and biological properties of guest molecules through labile interactions by formation of inclusion and/or association complexes. Plant cysteine proteinases from Caricaceae and Bromeliaceae are the subject of therapeutic interest, because of their anti-inflammatory, antitumoral, immunogenic, and wound-healing properties. In this study, we analyzed the association between beta-cyclodextrin (betaCD) and fraction P1G10 containing the bioactive proteinases from Carica candamarcensis, and described the physicochemical nature of the solid-state self-assembled complexes by Fourier transform infrared (FTIR) spectroscopy, thermogravimetry (TG), differential scanning calorimetry (DSC), X-ray powder diffraction (XRD), and nuclear magnetic resonance (NMR), as well as in solution by circular dichroism (CD), isothermal titration calorimetry (ITC), and amidase activity. The physicochemical analyses suggest the formation of a complex between P1G10 and betaCD. Higher secondary interactions, namely hydrophobic interactions, hydrogen bonding and van der Waals forces were observed at higher P1G10 : betaCD mass ratios. These results provide evidence of the occurrence of strong solid-state supramolecular non-covalent interactions between P1G10 and betaCD. Microcalorimetric analysis demonstrates that complexation results in a favorable enthalpic contribution, as has already been described during formation of similar betaCD inclusion compounds. The amidase activity of the complex shows that the enzyme activity is not readily available at 24 hours after dissolution of the complex in aqueous buffer; the proteinase becomes biologically active by the second day and remains stable until day 16, when a gradual decrease occurs, with basal activity attained by day 29. The reported results underscore the potential for betaCDs as candidates for complexing cysteine proteinases, resulting in supramolecular arrays with sustained proteolytic activity.

New developments in automated biosensing from remote water quality stations and satellite data retrieval for resources management

NASA Astrophysics Data System (ADS)

Morgan, E. L.; Eagleson, K. W.; Hermann, R.; McCollough, N. D.

1981-05-01

Maintaining adequate water quality in a multipurpose drainage system becomes increasingly important as demands on resources become greater. Real-time water quality monitoring plays a crucial role in meeting this objective. In addition to remote automated physical monitoring, developments at the end of the 1970's allow simultaneous real-time measurements of fish breathing response to water quality changes. These advantages complement complex in-stream surveys typically carried out to evaluate the environmental quality of a system. Automated biosensing units having remote capabilities are designed to aid in the evaluation of subtle water quality changes contributing to undesirable conditions in a drainage basin. Using microprocessor-based monitors to measure fish breathing rates, the biosensing units are interfaced to a U.S. National Aeronautics and Space Administration (N.A.S.A.) remote data collection platform for National Oceanic and Atmospheric Administration (N.O.A.A.) GOES satellite retrieval and transmission of data. Simultaneously, multiparameter physical information is collected from site-specific locations and recovered in a similar manner. Real-time biological and physical data received at a data processing center are readily available for interpretation by resource managers. Management schemes incorporating real-time monitoring networks into on-going programs to simultaneously retrieve biological and physical data by satellite, radio and telephone cable give added advantages in maintaining water quality for multipurpose needs.

Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II)

NASA Astrophysics Data System (ADS)

Singh, Bibhesh K.; Jetley, Umesh K.; Sharma, Rakesh K.; Garg, Bhagwan S.

2007-09-01

A new series of complexes of 2-hydroxy-3,5-dimethyl acetophenone oxime (HDMAOX) with Cu(II), Co(II), Ni(II) and Pd(II) have been prepared and characterized by different physical techniques. Infrared spectra of the complexes indicate deprotonation and coordination of the phenolic OH. It also confirms that nitrogen atom of the oximino group contributes to the complexation. Electronic spectra and magnetic susceptibility measurements reveal square planar geometry for Cu(II), Ni(II) and Pd(II) complexes and tetrahedral geometry for Co(II) complex. The elemental analyses and mass spectral data have justified the ML 2 composition of complexes. Kinetic and thermodynamic parameters were computed from the thermal decomposition data using Coats and Redfern method. The geometry of the metal complexes has been optimized with the help of molecular modeling. The free ligand (HDMAOX) and its metal complexes have been tested in vitro against Alternarie alternate, Aspergillus flavus, Aspergillus nidulans and Aspergillus niger fungi and Streptococcus, Staph, Staphylococcus and Escherchia coli bacteria in order to assess their antimicrobial potential. The results indicate that the ligand and its metal complexes possess antimicrobial properties.

Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II).

PubMed

Singh, Bibhesh K; Jetley, Umesh K; Sharma, Rakesh K; Garg, Bhagwan S

2007-09-01

A new series of complexes of 2-hydroxy-3,5-dimethyl acetophenone oxime (HDMAOX) with Cu(II), Co(II), Ni(II) and Pd(II) have been prepared and characterized by different physical techniques. Infrared spectra of the complexes indicate deprotonation and coordination of the phenolic OH. It also confirms that nitrogen atom of the oximino group contributes to the complexation. Electronic spectra and magnetic susceptibility measurements reveal square planar geometry for Cu(II), Ni(II) and Pd(II) complexes and tetrahedral geometry for Co(II) complex. The elemental analyses and mass spectral data have justified the ML(2) composition of complexes. Kinetic and thermodynamic parameters were computed from the thermal decomposition data using Coats and Redfern method. The geometry of the metal complexes has been optimized with the help of molecular modeling. The free ligand (HDMAOX) and its metal complexes have been tested in vitro against Alternarie alternate, Aspergillus flavus, Aspergillus nidulans and Aspergillus niger fungi and Streptococcus, Staph, Staphylococcus and Escherchia coli bacteria in order to assess their antimicrobial potential. The results indicate that the ligand and its metal complexes possess antimicrobial properties.

Biological aging and physical fitness in men aged 20-70 years from Kraków, Poland.

PubMed

Gołąb, Stanisław; Woronkowicz, Agnieszka; Kryst, Łukasz

2016-07-01

The increasing problem of population aging requires appropriate economic and health-related measures to mitigate its negative effects. The aim was to categorize the biological age of men between 20 and 70 years of age and assess its relationship to their physical activity and fitness. Data included morphological variables, total body water, the results of five Eurofit motor tests and the percentage of maximum heart rate (HR%), during a cardiovascular test of more than 1,400 20-70 year-old men living in Kraków. Biological age was estimated with regression equations. There were significant and consistent differences in physical fitness profiles between the three established groups of relations between biological and chronological age (biologically younger, equal, and older). These three categories of biological age were generally consistent with the regression analysis of physical fitness results, although declared physical activity seemed to be an independent factor. The selected morphological variables represent a set of characteristics useful for the determination of the biological age. The existing relationship between physical activity and biological age indicates that physical activity may contribute to the inhibition of involutional changes, even if it had only been performed regularly in the past. Am. J. Hum. Biol. 28:503-509, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Microfluidics and Cancer: Are we there yet?

PubMed Central

Zhang, Jennifer Zhuo; Nagrath, Sunitha

2013-01-01

More than two decades ago, microfluidics began to show its impact in biological research. Since then, the field of microfluidics has evolving rapidly. Cancer is one of the leading causes of death worldwide. Microfluidics holds great promise in cancer diagnosis and also serves as an emerging tool for understanding cancer biology. Microfluidics can be valuable for cancer investigation due to its high sensitivity, high throughput, less material-consumption, low cost, and enhanced spatio-temporal control. The physical laws on microscale offer an advantage enabling the control of physics, biology, chemistry and physiology at cellular level. Furthermore, microfluidic based platforms are portable and can be easily designed for point-of-care diagnostics. Developing and applying the state of the art microfluidic technologies to address the unmet challenges in cancer can expand the horizons of not only fundamental biology but also the management of disease and patient care. Despite the various microfluidic technologies available in the field, few have been tested clinically, which can be attributed to the various challenges existing in bridging the gap between the emerging technology and real world applications. We present a review of role of microlfuidcs in cancer research, including the history, recent advances and future directions to explore where the field stand currently in addressing complex clinical challenges and future of it. This review identifies four critical areas in cancer research, in which microfluidics can change the current paradigm. These include cancer cell isolation, molecular diagnostics, tumor biology and high-throughput screening for therapeutics. In addition, some of our lab’s current research is presented in the corresponding sections. PMID:23358873

Mosaic, Self-Similarity Logic, and Biological Attraction principles

PubMed Central

Baluška, František; Barlow, Peter W; Guidolin, Diego

2009-01-01

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal point of view, this type of organization is the result of a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course of this ‘passage through time, and suggest how today’s complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely the Mosaic, Self-Similarity Logic, and the Biological Attraction principles. Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatiotemporal level under consideration. The term Mosaic indicates how, from the same set of elements assembled according to different patterns, it is possible to arrive at completely different constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction is based on the evidence that each living organism creates an attractive field around itself. This field acts as a sphere of influence that actively attracts similar fields of other biological systems, thereby modifying salient features of the interacting organisms. Three specific organizational levels of living matter, namely the molecular, cellular, and supracellular levels, have been considered in order to analyse and illustrate the interpretative as well as the predictive roles of each of these three explanatory principles. PMID:20195461

S.E.A. Lab. Science Experiments and Activities. Marine Science for High School Students in Chemistry, Biology and Physics.

ERIC Educational Resources Information Center

Hart, Kathy, Ed.

A series of science experiments and activities designed for secondary school students taking biology, chemistry, physics, physical science or marine science courses are outlined. Each of the three major sections--chemistry, biology, and physics--addresses concepts that are generally covered in those courses but incorporates aspects of marine…

Learning Each Other's Ropes: Negotiating Interdisciplinary Authenticity

PubMed Central

Redish, Edward F.; Cooke, Todd J.

2013-01-01

A common feature of the recent calls for reform of the undergraduate biology curriculum has been for better coordination between biology and the courses from the allied disciplines of mathematics, chemistry, and physics. Physics has lagged behind math and chemistry in creating new, biologically oriented curricula, although much activity is now taking place, and significant progress is being made. In this essay, we consider a case study: a multiyear conversation between a physicist interested in adapting his physics course for biologists (E.F.R.) and a biologist interested in including more physics in his biology course (T.J.C.). These extended discussions have led us both to a deeper understanding of each other's discipline and to significant changes in the way we each think about and present our classes. We discuss two examples in detail: the creation of a physics problem on fluid flow for a biology class and the creation of a biologically authentic physics problem on scaling and dimensional analysis. In each case, we see differences in how the two disciplines frame and see value in the tasks. We conclude with some generalizations about how biology and physics look at the world differently that help us navigate the minefield of counterproductive stereotypical responses. PMID:23737626

Why is Physics Important to Cancer Research?

NASA Astrophysics Data System (ADS)

Barker, Anna D.

Cancer is increasingly described as a ''disease of the genes'', and while the genome (in fact all of the ``omes'') are important information molecules that drive aspects of the initiation and progression of cancer, they are far from the whole story. Cancer is an extraordinarily complex system (in fact a complex of systems) that occurs in three-dimensional space, across multiple scales - and often over extended periods of time. The most challenging issues that plague the cancer field such as metastasis, cellular heterogeneity and resistance to therapy are in large part more rationally explained in the context of the physics of these systems vs. genomics. For example, the biology of metastasis has been studied extensively for decades with little progress. Metastatic disease depends on cells acquiring (or expressing innate information) new properties that enable and sustain their ability to migrate to distant sites. Developing a fundamental understanding of key cancer processes ranging from metastasis to immunotherapeutic responses requires that physicists (and mathematicians and engineers) be integrated into a new generation of cancer research - period! The presentation will focus on those areas where physics is essential - and the how's and whose of achieving the integration required.

Thermostatted kinetic equations as models for complex systems in physics and life sciences.

PubMed

Bianca, Carlo

2012-12-01

Statistical mechanics is a powerful method for understanding equilibrium thermodynamics. An equivalent theoretical framework for nonequilibrium systems has remained elusive. The thermodynamic forces driving the system away from equilibrium introduce energy that must be dissipated if nonequilibrium steady states are to be obtained. Historically, further terms were introduced, collectively called a thermostat, whose original application was to generate constant-temperature equilibrium ensembles. This review surveys kinetic models coupled with time-reversible deterministic thermostats for the modeling of large systems composed both by inert matter particles and living entities. The introduction of deterministic thermostats allows to model the onset of nonequilibrium stationary states that are typical of most real-world complex systems. The first part of the paper is focused on a general presentation of the main physical and mathematical definitions and tools: nonequilibrium phenomena, Gauss least constraint principle and Gaussian thermostats. The second part provides a review of a variety of thermostatted mathematical models in physics and life sciences, including Kac, Boltzmann, Jager-Segel and the thermostatted (continuous and discrete) kinetic for active particles models. Applications refer to semiconductor devices, nanosciences, biological phenomena, vehicular traffic, social and economics systems, crowds and swarms dynamics. Copyright © 2012 Elsevier B.V. All rights reserved.

Preface

NASA Astrophysics Data System (ADS)

Mallamace, Francesco; Quintana, Jacqueline

2002-03-01

Complex systems represent one of the richest and more fascinating fields of current scientific research. The reason behind this is the important role that the properties of complex systems and materials play in a variety of different but overlapping areas in physics, chemistry, biology, mathematics, and social sciences, like medicine and economy. Such unusually broad research field is, therefore, of primary interest nowadays in pure science and technology. The role of statistical physics in this new field of complex systems has been present since its onset and it has been accelerating recently. Methods developed for studying ordering phenomena in simple systems have been generalized for application to more complex forms of matter (polymers, biological macromolecules, glasses, etc) and complex processes (e.g. chaos, turbulence, economy, jamming, biological processes). In particular, many different phenomena (considered in the past to belong to separate research fields) have now a common description. Pillars of such a description are the concepts of scaling and universality. The International Conference on `Scaling Concepts and Complex Systems' (a satellite meeting of STATPHYS21) was devoted to give an overview on recent developments around these two concepts. The Conference took place in Merida, Yucatan, Mexico, in July 9-14 2001. The meeting was held in the Gordon Conference style and was attended by about 100 scientists, it covered a large variety of theoretical and experimental research topics of current interest in complex systems and materials. The meeting consisted of a total number of about 40 invited and contributed talks and a poster session. The topics covered included: scaling behaviour, supra-molecular systems, aggregation, aggregation kinetics, growth mechanisms, disordered systems, soft condensed matter (polymers, biological polymers, bio-colloids, gels, colloids, membranes and interfacial phenomena), granular matter, phase separation and out-of-equilibrium dynamics, non-linear dynamics, chaos, turbulence and chaotic dynamics. The present issue contains a substantial number of the invited and contributed talks presented at the meeting. We made an effort to arrange these papers with an order similar to that of presentation during the meeting. It is our pleasure to thank the scientific committee, all the speakers, the session chairs and all participants who contributed to the success of the conference. We are grateful to the Bonino-Pulejo Foundation (Messina-Italy), and to the President On. Nino Calarco, for the Patronage and the enthusiastic support. Our thanks goes also for the Messina University, the INFM (Istituto Nazionale per la Fisica della Materia, Italy), the Consejo Nacional de Ciencia y Tecnología (CONACyT, Mexico) and the Universidad Nacional Autonoma de Mexico (UNAM). The Conference was sponsored by the INFM-Sec.C, CONACyT, UNAM, the Bonino-Pulejo Foundation which contributed financial support to participants and to the publication of the present issue. We are grateful to them for the support. Last, but not the least, we express our warmest gratitude to all the members of the local organizing committee for their assistance and for the work spent in organizing this meeting and especially to Professor~Alberto Robledo for his valuable advice.

Ionic interactions in biological and physical systems: a variational treatment.

PubMed

Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when enough data from disjoint experimental traditions are interpreted with a self-consistent theory.

Understanding Global Change (UGC) as a Unifying Conceptual Framework for Teaching Ecology: Using UGC in a High School Biology Program to Integrate Earth Science and Biology, and to Demonstrate the Value of Modeling Global Systems in Promoting Conceptual Learning

NASA Astrophysics Data System (ADS)

Levine, J.; Bean, J. R.

2017-12-01

Global change science is ideal for NGSS-informed teaching, but presents a serious challenge to K-12 educators because it is complex and interdisciplinary- combining earth science, biology, chemistry, and physics. Global systems are themselves complex. Adding anthropogenic influences on those systems creates a formidable list of topics - greenhouse effect, climate change, nitrogen enrichment, introduced species, land-use change among them - which are often presented as a disconnected "laundry list" of "facts." This complexity, combined with public and mass-media scientific illiteracy, leaves global change science vulnerable to misrepresentation and politicization, creating additional challenges to teachers in public schools. Ample stand-alone, one-off, online resources, many of them excellent, are (to date) underutilized by teachers in the high school science course taken by most students: biology. The Understanding Global Change project (UGC) from the UC Berkeley Museum of Paleontology has created a conceptual framework that organizes, connects, and explains global systems, human and non-human drivers of change in those systems, and measurable changes in those systems. This organization and framework employ core ideas, crosscutting concepts, structure/function relationships, and system models in a unique format that facilitates authentic understanding, rather than memorization. This system serves as an organizing framework for the entire ecology unit of a forthcoming mainstream high school biology program. The UGC system model is introduced up front with its core informational graphic. The model is elaborated, step by step, by adding concepts and processes as they are introduced and explained in each chapter. The informational graphic is thus used in several ways: to organize material as it is presented, to summarize topics in each chapter and put them in perspective, and for review and critical thinking exercises that supplement the usual end-of-chapter lists of key terms.

[Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands].

PubMed

Kostiukov, V V

2011-01-01

The energy contributions of various physical interactions to the total Gibbs energy of complex formation of the biologically important DNA hairpin d(GCGAAGC) with aromatic antitumor antibiotics daunomycin and novantron and the mutagens ethidium and proflavine have been calculated. It has been shown that the relatively small value of the total energy of binding of the ligands to the hairpin is the sum of components great in absolute value and different in sign. The contributions of van der Waals interactions and both intra- and intermolecular hydrogen bonds and bonds with aqueous environment have been studied. According to the calculations, the hydrophobic and van der Waals components are energetically favorable in complex formation of the ligands with the DNA pairpin d(GCGAAGC), whereas the electrostatic (with consideration of hydrogen bonds) and entropic components are unfavorable.

Rahman Prize Lecture: Lattice Boltzmann simulation of complex states of flowing matter

NASA Astrophysics Data System (ADS)

Succi, Sauro

Over the last three decades, the Lattice Boltzmann (LB) method has gained a prominent role in the numerical simulation of complex flows across an impressively broad range of scales, from fully-developed turbulence in real-life geometries, to multiphase flows in micro-fluidic devices, all the way down to biopolymer translocation in nanopores and lately, even quark-gluon plasmas. After a brief introduction to the main ideas behind the LB method and its historical developments, we shall present a few selected applications to complex flow problems at various scales of motion. Finally, we shall discuss prospects for extreme-scale LB simulations of outstanding problems in the physics of fluids and its interfaces with material sciences and biology, such as the modelling of fluid turbulence, the optimal design of nanoporous gold catalysts and protein folding/aggregation in crowded environments.

Complex-Shaped Microcomponents by the Reactive Conversion of Biology Templates

DTIC Science & Technology

2003-12-15

luminescent Eu-doped BaTiO3) and as structures for microfluidic mixing devices (e.g., based on electroosmotic flow). Optimization of the MgO conversion...ends of the iron tube. The tube was then crimped in the middle (to avoid physical mixing of the reactants) and the ends were welded shut. Upon heating...luminescent coatings (i.e., Eu-doped BaTiO 3 coatings on MgO), and ii) 3-D micro-structures for incorporation in electro-osmotic mixing devices (i.e., to

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis

PubMed Central

Awan, Imtiaz; Aziz, Wajid; Habib, Nazneen; Alowibdi, Jalal S.; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features. PMID:29771977

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis.

PubMed

Awan, Imtiaz; Aziz, Wajid; Shah, Imran Hussain; Habib, Nazneen; Alowibdi, Jalal S; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features.

The role of epigenetics in cardiovascular health and ageing: A focus on physical activity and nutrition.

PubMed

Wallace, Robert G; Twomey, Laura C; Custaud, Marc-Antoine; Turner, Jonathan D; Moyna, Niall; Cummins, Philip M; Murphy, Ronan P

2017-11-16

The cardiovascular system is responsible for transport of blood and nutrients to tissues, and is pivotal to the physiological health and longevity. Epigenetic modification is a natural, age-associated process resulting in highly contextualised gene expression with clear implications for cell differentiation and disease onset. Biological/epigenetic age is independent of chronological age, constituting a highly reflective snapshot of an individual's overall health. Accelerated vascular ageing is of major concern, effectively lowering disease threshold. Age-related chronic illness involves a complex interplay between many biological processes and is modulated by non-modifiable and modifiable risk factors. These alter the static genome by a number of epigenetic mechanisms, which change gene expression in an age and lifestyle dependent manner. This 'epigenetic drift' impacts health and contributes to the etiology of chronic illness. Lifestyle factors may cause acceleration of this epigenetic "clock", pre-disposing individuals to cardiovascular disease. Nutrition and physical activity are modifiable lifestyle choices, synergistically contributing to cardiovascular health. They represent a powerful potential epigenetic intervention point for effective cardiovascular protective and management strategies. Thus, together with traditional risk factors, monitoring the epigenetic signature of ageing may prove beneficial for tailoring lifestyle to fit biology - supporting the increasingly popular concept of "ageing well". Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids.

PubMed

Gumí-Audenis, Berta; Costa, Luca; Carlá, Francesco; Comin, Fabio; Sanz, Fausto; Giannotti, Marina I

2016-12-19

Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.

Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours

NASA Astrophysics Data System (ADS)

Batoulis, Helena; Schmidt, Thomas H.; Weber, Pascal; Schloetel, Jan-Gero; Kandt, Christian; Lang, Thorsten

2016-04-01

Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.

A study of the Alboran sea mesoscale system by means of empirical orthogonal function decomposition of satellite data

NASA Astrophysics Data System (ADS)

Baldacci, A.; Corsini, G.; Grasso, R.; Manzella, G.; Allen, J. T.; Cipollini, P.; Guymer, T. H.; Snaith, H. M.

2001-05-01

This paper presents the results of a combined empirical orthogonal function (EOF) analysis of Advanced Very High Resolution Radiometer (AVHRR) sea surface temperature (SST) data and sea-viewing wide field-of-view sensor (SeaWiFS) chlorophyll concentration data over the Alboran Sea (Western Mediterranean), covering a period of 1 year (November 1997-October 1998). The aim of this study is to go beyond the limited temporal extent of available in situ measurements by inferring the temporal and spatial variability of the Alboran Gyre system from long temporal series of satellite observations, in order to gain insight on the interactions between the circulation and the biological activity in the system. In this context, EOF decomposition permits concise and synoptic representation of the effects of physical and biological phenomena traced by SST and chlorophyll concentration. Thus, it is possible to focus the analysis on the most significant phenomena and to understand better the complex interactions between physics and biology at the mesoscale. The results of the EOF analysis of AVHRR-SST and SeaWiFS-chlorophyll concentration data are presented and discussed in detail. These improve and complement the knowledge acquired during the in situ observational campaigns of the MAST-III Observations and Modelling of Eddy scale Geostrophic and Ageostrophic motion (OMEGA) Project.

Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids

PubMed Central

Gumí-Audenis, Berta; Costa, Luca; Carlá, Francesco; Comin, Fabio; Sanz, Fausto; Giannotti, Marina I.

2016-01-01

Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information. PMID:27999368

Design, spectral characterization and biological studies of transition metal(II) complexes with triazole Schiff bases

NASA Astrophysics Data System (ADS)

Hanif, Muhammad; Chohan, Zahid H.

2013-03-01

A new series of three biologically active triazole derived Schiff base ligands L1-L3 have been synthesized in equimolar reaction of 3-amino-1H-1,2,4-triazole with pyrrol-2-carboxaldehyde, 4-bromo-thiophene-2-carboxaldehyde, and 5-iodo-2-hydroxy benzaldehyde. The prepared Schiff bases were used for further complex formation reaction with different metal elements like Co(II), Ni(II), Cu(II) and Zn(II) as chlorides by using a molar ratio of ligand:metal as 2:1. The structure and bonding nature of all the compounds were identified by their physical, spectral and analytical data. All the metal(II) complexes possessed an octahedral geometry except the Cu(II) complexes which showed a distorted octahedral geometry. All the synthesized compounds, were studied for their in vitro antibacterial, and antifungal activities, against four Gram-negative (Escherichia coli, Shigella sonnei, Pseudomonas aeruginosa and Salmonella typhi) and two Gram-positive (Bacillus subtilis and Staphylococcus aureus) bacterial strains and against six fungal strains (Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata) by using agar-well diffusion method. It has been shown that all the synthesized compounds showed moderate to significant antibacterial activity against one or more bacterial strains. In vitro Brine Shrimp bioassay was also carried out to investigate the cytotoxic properties of these compounds. The data also revealed that the metal complexes showed better activity than the ligands due to chelation/coordination.

The New Toxicology of Sophisticated Materials: Nanotoxicology and Beyond

PubMed Central

Maynard, Andrew D.; Warheit, David B.; Philbert, Martin A.

2011-01-01

It has long been recognized that the physical form of materials can mediate their toxicity—the health impacts of asbestiform materials, industrial aerosols, and ambient particulate matter are prime examples. Yet over the past 20 years, toxicology research has suggested complex and previously unrecognized associations between material physicochemistry at the nanoscale and biological interactions. With the rapid rise of the field of nanotechnology and the design and production of increasingly complex nanoscale materials, it has become ever more important to understand how the physical form and chemical composition of these materials interact synergistically to determine toxicity. As a result, a new field of research has emerged—nanotoxicology. Research within this field is highlighting the importance of material physicochemical properties in how dose is understood, how materials are characterized in a manner that enables quantitative data interpretation and comparison, and how materials move within, interact with, and are transformed by biological systems. Yet many of the substances that are the focus of current nanotoxicology studies are relatively simple materials that are at the vanguard of a new era of complex materials. Over the next 50 years, there will be a need to understand the toxicology of increasingly sophisticated materials that exhibit novel, dynamic and multifaceted functionality. If the toxicology community is to meet the challenge of ensuring the safe use of this new generation of substances, it will need to move beyond “nano” toxicology and toward a new toxicology of sophisticated materials. Here, we present a brief overview of the current state of the science on the toxicology of nanoscale materials and focus on three emerging toxicology-based challenges presented by sophisticated materials that will become increasingly important over the next 50 years: identifying relevant materials for study, physicochemical characterization, and biointeractions. PMID:21177774

Parameter Sensitivity and Laboratory Benchmarking of a Biogeochemical Process Model for Enhanced Anaerobic Dechlorination

NASA Astrophysics Data System (ADS)

Kouznetsova, I.; Gerhard, J. I.; Mao, X.; Barry, D. A.; Robinson, C.; Brovelli, A.; Harkness, M.; Fisher, A.; Mack, E. E.; Payne, J. A.; Dworatzek, S.; Roberts, J.

2008-12-01

A detailed model to simulate trichloroethene (TCE) dechlorination in anaerobic groundwater systems has been developed and implemented through PHAST, a robust and flexible geochemical modeling platform. The approach is comprehensive but retains flexibility such that models of varying complexity can be used to simulate TCE biodegradation in the vicinity of nonaqueous phase liquid (NAPL) source zones. The complete model considers a full suite of biological (e.g., dechlorination, fermentation, sulfate and iron reduction, electron donor competition, toxic inhibition, pH inhibition), physical (e.g., flow and mass transfer) and geochemical processes (e.g., pH modulation, gas formation, mineral interactions). Example simulations with the model demonstrated that the feedback between biological, physical, and geochemical processes is critical. Successful simulation of a thirty-two-month column experiment with site soil, complex groundwater chemistry, and exhibiting both anaerobic dechlorination and endogenous respiration, provided confidence in the modeling approach. A comprehensive suite of batch simulations was then conducted to estimate the sensitivity of predicted TCE degradation to the 36 model input parameters. A local sensitivity analysis was first employed to rank the importance of parameters, revealing that 5 parameters consistently dominated model predictions across a range of performance metrics. A global sensitivity analysis was then performed to evaluate the influence of a variety of full parameter data sets available in the literature. The modeling study was performed as part of the SABRE (Source Area BioREmediation) project, a public/private consortium whose charter is to determine if enhanced anaerobic bioremediation can result in effective and quantifiable treatment of chlorinated solvent DNAPL source areas. The modelling conducted has provided valuable insight into the complex interactions between processes in the evolving biogeochemical systems, particularly at the laboratory scale.

Physical and Biological Modes of Thought in the Chemistry of Linus Pauling

NASA Astrophysics Data System (ADS)

Nye, Mary Jo

No figure in modern chemistry better exemplifies than Linus Pauling (1901-1994) the intersections of the scientific disciplines of chemistry, physics, and biology nor the roles of physical and biological modes of thought in the 'central science' of chemistry.

42 CFR 493.1449 - Standard; Technical supervisor qualifications.

Code of Federal Regulations, 2010 CFR

2010-10-01

... earned doctoral degree in a chemical, physical, biological or clinical laboratory science from an... chemical, physical, biological or clinical laboratory science or medical technology from an accredited..., physical, or biological science or medical technology from an accredited institution; and (ii) Have at...

42 CFR 493.1449 - Standard; Technical supervisor qualifications.

Code of Federal Regulations, 2012 CFR

2012-10-01

... earned doctoral degree in a chemical, physical, biological or clinical laboratory science from an... chemical, physical, biological or clinical laboratory science or medical technology from an accredited..., physical, or biological science or medical technology from an accredited institution; and (ii) Have at...

42 CFR 493.1449 - Standard; Technical supervisor qualifications.

Code of Federal Regulations, 2014 CFR

2014-10-01

... earned doctoral degree in a chemical, physical, biological or clinical laboratory science from an... chemical, physical, biological or clinical laboratory science or medical technology from an accredited..., physical, or biological science or medical technology from an accredited institution; and (ii) Have at...

42 CFR 493.1449 - Standard; Technical supervisor qualifications.

Code of Federal Regulations, 2013 CFR

2013-10-01

... earned doctoral degree in a chemical, physical, biological or clinical laboratory science from an... chemical, physical, biological or clinical laboratory science or medical technology from an accredited..., physical, or biological science or medical technology from an accredited institution; and (ii) Have at...

Integrative mental health care: from theory to practice, Part 2.

PubMed

Lake, James

2008-01-01

Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examined the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discussed implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology, for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understanding of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

Integrative mental health care: from theory to practice, part 1.

PubMed

Lake, James

2007-01-01

Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examines the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discusses implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understandings of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

Characterization of the influence of external stimulus on protein-nucleic acid complex through multiscale computations

NASA Astrophysics Data System (ADS)

Gosai, Agnivo

The concomitant detection, monitoring and analysis of biomolecules have assumed utmost importance in the field of medical diagnostics as well as in different spheres of biotechnology research such as drug development, environmental hazard detection and biodefense. There is an increased demand for the modulation of the biological response for such detection / sensing schemes which will be facilitated by the sensitive and controllable transmission of external stimuli. Electrostatic actuation for the controlled release/capture of biomolecules through conformational transformations of bioreceptors provides an efficient and feasible mechanism to modulate biological response. In addition, electrostatic actuation mechanism has the advantage of allowing massively parallel schemes and measurement capabilities that could ultimately be essential for biomedical applications. Experiments have previously demonstrated the unbinding of thrombin from its aptamer in presence of small positive electrode potential whereas the complex remained associated in presence of small negative potentials / zero potential. However, the nanoscale physics/chemistry involved in this process is not clearly understood. In this thesis a combination of continuum mechanics based modeling and a variety of atomistic simulation techniques have been utilized to corroborate the aforementioned experimental observations. It is found that the computational approach can satisfactorily predict the dynamics of the electrically excited aptamer-thrombin complex as well as provide an analytical model to characterize the forced binding of the complex.

At a glance: cellular biology for engineers.

PubMed

Khoshmanesh, K; Kouzani, A Z; Nahavandi, S; Baratchi, S; Kanwar, J R

2008-10-01

Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper aims to overcome this bottleneck by describing the human cell components as micro-plants that form cells as micro-bio-factories. This concept can accelerate the engineers' comprehension of the subject. In this paper, first the structure and function of different cell components are described. In addition, the engineering attempts to mimic various cell components through numerical modelling or physical implementation are highlighted. Next, the interaction of different cell components that facilitate complicated chemical processes, such as energy generation and protein synthesis, are described. These complex interactions are translated into simple flow diagrams, generally used by engineers to represent multi-component processes.

Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws.

PubMed

Auffray, Charles; Nottale, Laurent

2008-05-01

In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, and discuss how scale laws of increasing complexity can be used to model and understand the behaviour of complex biological systems. In scale relativity theory, the geometry of space is considered to be continuous but non-differentiable, therefore fractal (i.e., explicitly scale-dependent). One writes the equations of motion in such a space as geodesics equations, under the constraint of the principle of relativity of all scales in nature. To this purpose, covariant derivatives are constructed that implement the various effects of the non-differentiable and fractal geometry. In this first review paper, the scale laws that describe the new dependence on resolutions of physical quantities are obtained as solutions of differential equations acting in the scale space. This leads to several possible levels of description for these laws, from the simplest scale invariant laws to generalized laws with variable fractal dimensions. Initial applications of these laws to the study of species evolution, embryogenesis and cell confinement are discussed.

Development of hydrogels for regenerative engineering.

PubMed

Guan, Xiaofei; Avci-Adali, Meltem; Alarçin, Emine; Cheng, Hao; Kashaf, Sara Saheb; Li, Yuxiao; Chawla, Aditya; Jang, Hae Lin; Khademhosseini, Ali

2017-05-01

The aim of regenerative engineering is to restore complex tissues and biological systems through convergence in the fields of advanced biomaterials, stem cell science, and developmental biology. Hydrogels are one of the most attractive biomaterials for regenerative engineering, since they can be engineered into tissue mimetic 3D scaffolds to support cell growth due to their similarity to native extracellular matrix. Advanced nano- and micro-technologies have dramatically increased the ability to control properties and functionalities of hydrogel materials by facilitating biomimetic fabrication of more sophisticated compositions and architectures, thus extending our understanding of cell-matrix interactions at the nanoscale. With this perspective, this review discusses the most commonly used hydrogel materials and their fabrication strategies for regenerative engineering. We highlight the physical, chemical, and functional modulation of hydrogels to design and engineer biomimetic tissues based on recent achievements in nano- and micro-technologies. In addition, current hydrogel-based regenerative engineering strategies for treating multiple tissues, such as musculoskeletal, nervous and cardiac tissue, are also covered in this review. The interaction of multiple disciplines including materials science, cell biology, and chemistry, will further play an important role in the design of functional hydrogels for the regeneration of complex tissues. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

78 FR 58311 - Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

...] Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop; Request for... Issues in Developing Drug and Biological Products for Rare Diseases.'' The purpose of the public workshop is twofold: To discuss complex issues in clinical trials for developing drug and biological products...

Introductory physics in biological context: An approach to improve introductory physics for life science students

NASA Astrophysics Data System (ADS)

Crouch, Catherine H.; Heller, Kenneth

2014-05-01

We describe restructuring the introductory physics for life science students (IPLS) course to better support these students in using physics to understand their chosen fields. Our courses teach physics using biologically rich contexts. Specifically, we use examples in which fundamental physics contributes significantly to understanding a biological system to make explicit the value of physics to the life sciences. This requires selecting the course content to reflect the topics most relevant to biology while maintaining the fundamental disciplinary structure of physics. In addition to stressing the importance of the fundamental principles of physics, an important goal is developing students' quantitative and problem solving skills. Our guiding pedagogical framework is the cognitive apprenticeship model, in which learning occurs most effectively when students can articulate why what they are learning matters to them. In this article, we describe our courses, summarize initial assessment data, and identify needs for future research.

Conception and development of the Second Life® Embryo Physics Course.

PubMed

Gordon, Richard

2013-06-01

The study of embryos with the tools and mindset of physics, started by Wilhelm His in the 1880s, has resumed after a hiatus of a century. The Embryo Physics Course convenes online allowing interested researchers and students, who are scattered around the world, to gather weekly in one place, the virtual world of Second Life®. It attracts people from a wide variety of disciplines and walks of life: applied mathematics, artificial life, bioengineering, biophysics, cancer biology, cellular automata, civil engineering, computer science, embryology, electrical engineering, evolution, finite element methods, history of biology, human genetics, mathematics, molecular developmental biology, molecular biology, nanotechnology, philosophy of biology, phycology, physics, self-reproducing systems, stem cells, tensegrity structures, theoretical biology, and tissue engineering. Now in its fifth year, the Embryo Physics Course provides a focus for research on the central question of how an embryo builds itself.

The Interface between Physics and Biology: An Unexplored Territory.

ERIC Educational Resources Information Center

Marx, George

1980-01-01

Discusses from the physicist's point of view the connection between biology and physics and the usefulness of physical laws for understanding biological processes. Discusses these fields of research in secondary school science: molecular science, regulation, statistics and information, corrosion and evolution, chance and necessity, and…

New mixed ligand cobalt(II/III) complexes based on the drug sodium valproate and bioactive nitrogen-donor ligands. Synthesis, structure and biological properties

NASA Astrophysics Data System (ADS)

Abu Ali, Hijazi; Abu Shamma, Amani; Kamel, Shayma

2017-08-01

New cobalt valproate complexes with different nitrogen based ligands were synthesized and characterized using various techniques such as IR, UV-Vis, single crystal X-ray diffraction as well as other physical properties. The general formula of the prepared complexes is [Con(valp)m(L)z], (n = 1, 2 …; m = 1, 2, …; Z = 1, 2 …). The complexes [Co2(valp)4] (1), [Co(valp)2(2-ampy)2] (2) and [Co2(valp)4(quin)2] (3) showed different carboxylate coordination modes. The crystal structures of the complexes 2 and 3 were determined using single crystal X-ray diffraction. Kinetic studies of hydrolysis reactions of BNPP [bis-(p-nitrophenyl)phosphate] with complexes 2 and 3 were performed. The hydrolysis rate of BNPP was studied at different temperatures, pH and concentrations by UV-Vis spectrophotometric method. The results showed that the hydrolysis rate of BNPP was 7.70 × 102 L mol-1 s-1 for (3) and 2.60 × 10-1 L mol-1 s-1 for (2).

Quantum Dot Surface Engineering: Toward Inert Fluorophores with Compact Size and Bright, Stable Emission

PubMed Central

Lim, Sung Jun; Ma, Liang; Schleife, André; Smith, Andrew M.

2016-01-01

The surfaces of colloidal nanocrystals are complex interfaces between solid crystals, coordinating ligands, and liquid solutions. For fluorescent quantum dots, the properties of the surface vastly influence the efficiency of light emission, stability, and physical interactions, and thus determine their sensitivity and specificity when they are used to detect and image biological molecules. But after more than 30 years of study, the surfaces of quantum dots remain poorly understood and continue to be an important subject of both experimental and theoretical research. In this article, we review the physics and chemistry of quantum dot surfaces and describe approaches to engineer optimal fluorescent probes for applications in biomolecular imaging and sensing. We describe the structure and electronic properties of crystalline facets, the chemistry of ligand coordination, and the impact of ligands on optical properties. We further describe recent advances in compact coatings that have significantly improved their properties by providing small hydrodynamic size, high stability and fluorescence efficiency, and minimal nonspecific interactions with cells and biological molecules. While major progress has been made in both basic and applied research, many questions remain in the chemistry and physics of quantum dot surfaces that have hindered key breakthroughs to fully optimize their properties. PMID:28344357

Climate change and coastal environmental risk perceptions in Florida.

PubMed

Carlton, Stuart J; Jacobson, Susan K

2013-11-30

Understanding public perceptions of climate change risks is a prerequisite for effective climate communication and adaptation. Many studies of climate risk perceptions have either analyzed a general operationalization of climate change risk or employed a case-study approach of specific adaptive processes. This study takes a different approach, examining attitudes toward 17 specific, climate-related coastal risks and cognitive, affective, and risk-specific predictors of risk perception. A survey of 558 undergraduates revealed that risks to the physical environment were a greater concern than economic or biological risks. Perceptions of greater physical environment risks were significantly associated with having more pro-environmental attitudes, being female, and being more Democratic-leaning. Perceptions of greater economic risks were significantly associated with having more negative environmental attitudes, being female, and being more Republican-leaning. Perceptions of greater biological risks were significantly associated with more positive environmental attitudes. The findings suggest that focusing on physical environment risks maybe more salient to this audience than communications about general climate change adaptation. The results demonstrate that climate change beliefs and risk perceptions are multifactorial and complex and are shaped by individuals' attitudes and basic beliefs. Climate risk communications need to apply this knowledge to better target cognitive and affective processes of specific audiences, rather than providing simple characterizations of risks. Copyright © 2013 Elsevier Ltd. All rights reserved.

75 FR 14565 - NIST Summer Institute for Middle School Science Teachers; Availability of Funds

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-26

...), including, but not limited to, earth science, physical science, chemistry, physics, and/or biology. This... science, physical science, chemistry, physics and/or biology. NIST will award funding that will support... instruction in general science fields including earth science, physical science, chemistry, physics, and/or...

Soil Quality Indexing Strategies for Evaluating Sugarcane Expansion in Brazil

PubMed Central

Cherubin, Maurício R.; Karlen, Douglas L.; Cerri, Carlos E. P.; Franco, André L. C.; Tormena, Cássio A.; Davies, Christian A.; Cerri, Carlos C.

2016-01-01

Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time. PMID:26938642

Soil Quality Indexing Strategies for Evaluating Sugarcane Expansion in Brazil.

PubMed

Cherubin, Maurício R; Karlen, Douglas L; Cerri, Carlos E P; Franco, André L C; Tormena, Cássio A; Davies, Christian A; Cerri, Carlos C

2016-01-01

Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time.

14 CFR 1275.101 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., biology, engineering and physical sciences (physics and chemistry). (h) Inquiry means the assessment of..., social sciences, statistics, and biological and physical research (ground based and microgravity...

Molecules in interstellar clouds. [physical and chemical conditions of star formation and biological evolution

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Hjalmarson, A.; Rydbeck, O. E. H.

1981-01-01

The physical conditions and chemical compositions of the gas in interstellar clouds are reviewed in light of the importance of interstellar clouds for star formation and the origin of life. The Orion A region is discussed as an example of a giant molecular cloud where massive stars are being formed, and it is pointed out that conditions in the core of the cloud, with a kinetic temperature of about 75 K and a density of 100,000-1,000,000 molecules/cu cm, may support gas phase ion-molecule chemistry. The Taurus Molecular Clouds are then considered as examples of cold, dark, relatively dense interstellar clouds which may be the birthplaces of solar-type stars and which have been found to contain the heaviest interstellar molecules yet discovered. The molecular species identified in each of these regions are tabulated, including such building blocks of biological monomers as H2O, NH3, H2CO, CO, H2S, CH3CN and H2, and more complex species such as HCOOCH3 and CH3CH2CN.

[In vitro renaturation of proteins from inclusion bodies].

PubMed

Porowińska, Dorota; Marszałek, Ewelina; Wardęcka, Paulina; Komoszyński, Michał

2012-06-11

Recombinant proteins and enzymes are commonly used in many areas of our life, such as diagnostics, industry and medicine, due to heterologous synthesis in prokaryotic expression systems. However, a high expression level of foreign protein in bacteria cells results in formation of inactive and insoluble aggregates--inclusion bodies. Reactivation of aggregated proteins is a complex and time-consuming process. Every protein requires experimental optimization of the process conditions. The choice of the refolding method depends on the type of recombinant protein and its physical, chemical and biological properties. Recovery of the activity of proteins accumulated in inclusion bodies can be divided into 4 steps: 1) inclusion bodies isolation, 2) solubilization of aggregates, 3) renaturation, 4) purification of catalytically active molecules. Efficiency of the refolding process depends on many physical factors and chemical and biological agents. The above parameters determine the time of the folding and prevent protein aggregation. They also assist the folding and have an influence on the solubility and stability of native molecules. To date, dilution, dialysis and chromatography are the most often used methods for protein refolding.

The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs?

PubMed

Maggiora, Gerald M

2011-08-01

Reductionism is alive and well in drug-discovery research. In that tradition, we continually improve experimental and computational methods for studying smaller and smaller aspects of biological systems. Although significant improvements continue to be made, are our efforts too narrowly focused? Suppose all error could be removed from these methods, would we then understand biological systems sufficiently well to design effective drugs? Currently, almost all drug research focuses on single targets. Should the process be expanded to include multiple targets? Recent efforts in this direction have lead to the emerging field of polypharmacology. This appears to be a move in the right direction, but how much polypharmacology is enough? As the complexity of the processes underlying polypharmacology increase will we be able to understand them and their inter-relationships? Is "new" mathematics unfamiliar in much of physics and chemistry research needed to accomplish this task? A number of these questions will be addressed in this paper, which focuses on issues and questions not answers to the drug-discovery conundrum.

Analyzing the substitution effect on the CoMFA results within the framework of density functional theory (DFT).

PubMed

Morales-Bayuelo, Alejandro

2016-07-01

Though QSAR was originally developed in the context of physical organic chemistry, it has been applied very extensively to chemicals (drugs) which act on biological systems, in this idea one of the most important QSAR methods is the 3D QSAR model. However, due to the complexity of understanding the results it is necessary to postulate new methodologies to highlight their physical-chemical meaning. In this sense, this work postulates new insights to understand the CoMFA results using molecular quantum similarity and chemical reactivity descriptors within the framework of density functional theory. To obtain these insights a simple theoretical scheme involving quantum similarity (overlap, coulomb operators, their euclidean distances) and chemical reactivity descriptors such as chemical potential (μ), hardness (ɳ), softness (S), electrophilicity (ω), and the Fukui functions, was used to understand the substitution effect. In this sense, this methodology can be applied to analyze the biological activity and the stabilization process in the non-covalent interactions on a particular molecular set taking a reference compound.

A Course of Coordinated Sciences: The Structure of Matter

ERIC Educational Resources Information Center

Mannino, S.; And Others

1976-01-01

Describes a three-year coordinated sciences course taught to Italian high school students by physics and biology teachers and biology, physics, and psychology faculty from the University of Palermo. The course examines the structure of matter and energy from physical, biological, chemical, economical, and historical viewpoints. (MLH)

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes.

PubMed

Srihari, Sriganesh; Yong, Chern Han; Patil, Ashwini; Wong, Limsoon

2015-09-14

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight their limitations and challenges, in particular at detecting sparse and small or sub-complexes and discerning overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A Cluster Randomized Controlled Trial on the Effects of Technology-aided Testing and Feedback on Physical Activity and Biological Age Among Employees in a Medium-sized Enterprise.

PubMed

Liukkonen, Mika; Nygård, Clas-Håkan; Laukkanen, Raija

2017-12-01

It has been suggested that engaging technology can empower individuals to be more proactive about their health and reduce their health risks. The aim of the present intervention was to study the effects of technology-aided testing and feedback on physical activity and biological age of employees in a middle-sized enterprise. In all, 121 employees (mean age 42 ± 10 years) participated in the 12-month three-arm cluster randomized trial. The fitness measurement process (Body Age) determined the participants' biological age in years. Physical activity was measured with the International Physical Activity Questionnaire Short Form. Physical activity did not change during the intervention. Biological age (better fitness) improved in all groups statistically significantly ( p  < 0.001), but with no interaction effects. The mean changes (years) in the groups were -2.20 for the controls, -2.83 for the group receiving their biological age and feedback, and -2.31 for the group receiving their biological age, feedback, and a training computer. Technology-aided testing with feedback does not seem to change the amount of physical activity but may enhance physical fitness measured by biological age.

Biomimetic Phases of Microtubule-Motor Mixtures

NASA Astrophysics Data System (ADS)

Ross, Jennifer

2014-03-01

We try to determine the universal principles of organization from the molecular scale that gives rise to architecture on the cellular scale. We are specifically interested in the organization of the microtubule cytoskeleton, a rigid, yet versatile network in most cell types. Microtubules in the cell are organized by motor proteins and crosslinkers. This work applies the ideas of statistical mechanics and condensed matter physics to the non-equilibrium pattern formation behind intracellular organization using the microtubule cytoskeleton as the building blocks. We examine these processes in a bottom-up manner by adding increasingly complex protein actors into the system. Our systematic experiments expose nature's laws for organization and has large impacts on biology as well as illuminating new frontiers of non-equilibrium physics.

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.

PubMed

Havugimana, Pierre C; Hu, Pingzhao; Emili, Andrew

2017-10-01

Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools - most notably machine learning - that allow for the generation of high-quality protein association maps. Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups' ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts.

Statistical physics of the symmetric group.

PubMed

Williams, Mobolaji

2017-04-01

Ordered chains (such as chains of amino acids) are ubiquitous in biological cells, and these chains perform specific functions contingent on the sequence of their components. Using the existence and general properties of such sequences as a theoretical motivation, we study the statistical physics of systems whose state space is defined by the possible permutations of an ordered list, i.e., the symmetric group, and whose energy is a function of how certain permutations deviate from some chosen correct ordering. Such a nonfactorizable state space is quite different from the state spaces typically considered in statistical physics systems and consequently has novel behavior in systems with interacting and even noninteracting Hamiltonians. Various parameter choices of a mean-field model reveal the system to contain five different physical regimes defined by two transition temperatures, a triple point, and a quadruple point. Finally, we conclude by discussing how the general analysis can be extended to state spaces with more complex combinatorial properties and to other standard questions of statistical mechanics models.

Universal physical responses to stretch in the living cell

PubMed Central

Trepat, Xavier; Deng, Linhong; An, Steven S.; Navajas, Daniel; Tschumperlin, Daniel J.; Gerthoffer, William T.; Butler, James P.; Fredberg, Jeffrey J.

2008-01-01

With every beat of the heart, inflation of the lung or peristalsis of the gut, cell types of diverse function are subjected to substantial stretch. Stretch is a potent stimulus for growth, differentiation, migration, remodelling and gene expression1,2. Here, we report that in response to transient stretch the cytoskeleton fluidizes in such a way as to define a universal response class. This finding implicates mechanisms mediated not only by specific signalling intermediates, as is usually assumed, but also by non-specific actions of a slowly evolving network of physical forces. These results support the idea that the cell interior is at once a crowded chemical space3 and a fragile soft material in which the effects of biochemistry, molecular crowding and physical forces are complex and inseparable, yet conspire nonetheless to yield remarkably simple phenomenological laws. These laws seem to be both universal and primitive, and thus comprise a striking intersection between the worlds of cell biology and soft matter physics. PMID:17538621

Statistical physics of the symmetric group

NASA Astrophysics Data System (ADS)

Williams, Mobolaji

2017-04-01

Ordered chains (such as chains of amino acids) are ubiquitous in biological cells, and these chains perform specific functions contingent on the sequence of their components. Using the existence and general properties of such sequences as a theoretical motivation, we study the statistical physics of systems whose state space is defined by the possible permutations of an ordered list, i.e., the symmetric group, and whose energy is a function of how certain permutations deviate from some chosen correct ordering. Such a nonfactorizable state space is quite different from the state spaces typically considered in statistical physics systems and consequently has novel behavior in systems with interacting and even noninteracting Hamiltonians. Various parameter choices of a mean-field model reveal the system to contain five different physical regimes defined by two transition temperatures, a triple point, and a quadruple point. Finally, we conclude by discussing how the general analysis can be extended to state spaces with more complex combinatorial properties and to other standard questions of statistical mechanics models.

The universal ancestor

NASA Technical Reports Server (NTRS)

Woese, C.

1998-01-01

A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

14 CFR § 1275.101 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., biology, engineering and physical sciences (physics and chemistry). (h) Inquiry means the assessment of..., psychology, social sciences, statistics, and biological and physical research (ground based and microgravity...

Biological/Genetic Regulation of Physical Activity Level: Consensus from GenBioPAC.

PubMed

Lightfoot, J Timothy; DE Geus, Eco J C; Booth, Frank W; Bray, Molly S; DEN Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

2018-04-01

Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors; however, a growing body of literature suggests that biological determinants play a significant role in regulating physical activity levels. For instance, physical activity level, measured in various manners, has a genetic component in both humans and nonhuman animal models. This consensus article, developed as a result of an American College of Sports Medicine-sponsored round table, provides a brief review of the theoretical concepts and existing literature that supports a significant role of genetic and other biological factors in the regulation of physical activity. Future research on physical activity regulation should incorporate genetics and other biological determinants of physical activity instead of a sole reliance on social and other environmental determinants.

[Pressing problems of labor hygiene and occupational pathology among office workers].

PubMed

Dudarev, A A; Sorokin, G A

2012-01-01

Northwest public health research center, Ministry of health and social affairs, St.-Petersburg. The article substantiates the conception of "office room", "office worker", estimates the basic diseases and symptoms among office workers (SBS-syndrome, BRI-illnesses, BRS-symptoms). Complex of indoor factors of office environment are analyzed, which influence the health status of personnel--indoor air quality (microclimate, aerosols, chemical, biological pollution, air ionization), external physical factors, ergonomics, intensity and tension of work, psychosocial factors. Comparison of Russian and foreign approaches to the hygienic estimation and rating of these factors was carried out. Owing to inadequacy of Russian hygienic rules to modern requirements, the necessity of working out of a complex of sanitary rules focused particularly on office workers is proved.

[Cerebrospinal fluid diagnostics in Germany since 1950 : Developments in the GDR and FRG in the context of society and science].

PubMed

Reiber, H

2016-12-01

The 40 years of separated development in two countries with extremely different political and social utopias allow consideration of the connection between science and society. The society-dependent development of cerebrospinal fluid (CSF) diagnostics in the German Democratic Republic (GDR) and the Federal Republic of Germany (FRG) is shown in the context of the international scientific development of the post-war era with new paradigms in physics, biology and genetics. As part of this contribution to the philosophy of science the consequences of the complex life science for a new view of disease research are discussed in contrast to the currently dominating, reductionistic medical industrial complex.

Tails and Ties. Editorial

NASA Astrophysics Data System (ADS)

Carbone, A.; Kaniadakis, G.; Scarfone, A. M.

2007-05-01

The study of behavioural and social phenomena has experienced a surge of interest over the last decade. One reason for this great attention is the huge amount of high quality data made available by the internet technologies. The many studies spanning concepts and problems belonging to economics, biology, ecology, physics and computer science, clearly indicates increasing interdisciplinary cross-fertilization, commonalities in the different approaches and communication across these disciplines. This issue of The European Physical Journal B is devoted to the interdisciplinary field of Sociophysics. The papers have been selected from the contributions presented at the 5th International Conference on “Applications of Physics in Financial Analysis" (APFA5) held in Torino from June 29th to July 1st 2006 ( http://www.polito.it/apfa5). The synergy and richness of results obtained from the investigation of problems belonging to the area of complexity science from different perspectives clearly indicates future directions and research methodologies in this field.

Juvenile Fibromyalgia: A Multidisciplinary Approach to Treatment.

PubMed

Tesher, Melissa S

2015-06-01

A 14-year-old boy presented with months of severe widespread musculoskeletal pain. He was profoundly fatigued and unable to attend school. Laboratory evaluation, including complete blood count, comprehensive metabolic panel, inflammatory markers, and thyroid function, was unrevealing. Physical examination was also normal except for multiple tender points. The patient was diagnosed with juvenile primary fibromyalgia syndrome and referred for multidisciplinary treatment including physical therapy, exercise, and counseling, and his daily functioning gradually improves. Juvenile fibromyalgia is a complex syndrome that often severely limits patients' activities and can impede normal adolescent development. Effective treatment requires an understanding of the biologic, psychologic, and social factors contributing to the perpetuation of chronic pain. The author reviews the diagnostic criteria, pathophysiology, and treatment of juvenile fibromyalgia. Medications, particularly antidepressants and anticonvulsants, can be useful adjuncts to therapy. However, multimodal pain management including intensive physical therapy, exercise, counseling, and sleep hygiene is most effective in treating fibromyalgia. Copyright 2015, SLACK Incorporated.

Two sides of the coin. Part 2. Colloid and surface science meets real biointerfaces.

PubMed

Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

2017-11-01

Part 1 revisited developments in lipid and surfactant self assembly over the past 40 years [1]. New concepts emerged. Here we explore how these developments can be used to make sense of and bring order to a range of complex biological phenomena. Together with Part 1, this contribution is a fundamental revision of intuition at the boundaries of Colloid Science and Biological interfaces from a perspective of nearly 50 years. We offer new insights on a unified treatment of self assembly of lipids, surfactants and proteins in the light of developments presented in Part 1. These were in the enabling disciplines in molecular forces, hydration, oil and electrolyte specificity; and in the role of non Euclidean geometries-across the whole gammut of physical, colloid and surface chemistry, biophysics and membrane biology and medicine. It is where the early founders of the cell theory of biology and the physiologists expected advances to occur as D'Arcy Thompson predicted us 100 years ago. Copyright © 2017 Elsevier B.V. All rights reserved.

Using dynamics to identify network topology

NASA Astrophysics Data System (ADS)

Rahi, Sahand Jamal; Tsaneva-Atanasova, Krasimira

2013-03-01

To elucidate the topology of a signaling pathway, generally, experimentalists manipulate a cell's molecular architecture, for example, by knocking out genes. Molecular biology techniques, though, are not only invasive and labor-intensive, they have also often been eluded by the complexity of biological networks, e.g., in the case of the gonadotropin-releasing hormone (GnRH) system. Inspired by the rapidly accumulating examples of oscillatory signaling in biology, we explored whether such dynamical stimuli can be used to discriminate different topologies of adaptive pathways, which are ubiquitous in biology. Responses to static inputs are nearly indistinguishable given strong measurement noise. Sine function stimuli, widely used in physics, are difficult to implement in standard microfluidics or optogenetics set-ups and do not simplify the mathematical analysis because of the nonlinearities in these systems. With periodic on-off pulses, which can be easily produced, however, simple adaptive circuit motifs and detailed models from the literature robustly reveal distinct output characteristics, which manifest in how the period of maximal output varies with pulse width. Our calculations provide a framework for using existing methods to discover difficult to reveal mechanisms. Furthermore, our results constrain the possible design principles of the presumed frequency decoders in biological systems where pulsatile signaling has recently been discovered.

Fluorescence fluctuations analysis in nanoapertures: physical concepts and biological applications.

PubMed

Lenne, Pierre-François; Rigneault, Hervé; Marguet, Didier; Wenger, Jérôme

2008-11-01

During the past years, nanophotonics has provided new approaches to study the biological processes below the optical diffraction limit. How single molecules diffuse, bind and assemble can be studied now at the nanometric level, not only in solutions but also in complex and crowded environments such as in live cells. In this context fluorescence fluctuations spectroscopy is a unique tool since it has proven to be easy to use in combination with nanostructures, which are able to confine light in nanometric volumes. We review here recent advances in fluorescence fluctuations' analysis below the optical diffraction limit with a special focus on nanoapertures milled in metallic films. We discuss applications in the field of single-molecule detection, DNA sequencing and membrane organization, and underscore some potential perspectives of this new emerging technology.

Biofabrication and biomaterials for urinary tract reconstruction

PubMed Central

Elsawy, Moustafa M; de Mel, Achala

2017-01-01

Reconstructive urologists are constantly facing diverse and complex pathologies that require structural and functional restoration of urinary organs. There is always a demand for a biocompatible material to repair or substitute the urinary tract instead of using patient’s autologous tissues with its associated morbidity. Biomimetic approaches are tissue-engineering tactics aiming to tailor the material physical and biological properties to behave physiologically similar to the urinary system. This review highlights the different strategies to mimic urinary tissues including modifications in structure, surface chemistry, and cellular response of a range of biological and synthetic materials. The article also outlines the measures to minimize infectious complications, which might lead to graft failure. Relevant experimental and preclinical studies are discussed, as well as promising biomimetic approaches such as three-dimensional bioprinting. PMID:28546955

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and its Application in Life Sciences

NASA Astrophysics Data System (ADS)

Xu, Gu-feng; Wang, Hong-mei

2001-08-01

Inductively-coupled plasma mass spectrometry (ICP-MS) has made much progress since its birth in the late 1990s. This paper will give a rather systematic overview on the use of this technique in new devices and technologies related to plasma source, sample-introducing device and detecting spectrometer etc. In this overview, an emphasis will be put on the evaluation of the ICP-MS technique in combination with a series of physical, chemical and biological techniques, such as laser ablation (LA), capillary electrophoresis (CE) and high performance liquid chromatograph (HPLC), along with their representative high accuracy and high sensitivity. Finally, comprehensive and fruitful applications of the ICP-MS and its combinative techniques in the detection of trace metallic elements and isotopes in complex biological and environmental samples will be revealed.

Synthesis and property investigation of metal-based nanomaterials for biotechnological applications

NASA Astrophysics Data System (ADS)

Darsanasiri, Nalin Dammika

Luminescent lanthanide-based materials have drawn recent interest due to their applications in in vitro cellular imaging. Sensitive biological analysis requires optical labels with high water dispersibility & stability and excellent luminescent properties. Most literature reported lanthanide complexes with high luminescence intensity are hydrophobic and unstable, limiting their biological applications. This project was designed to incorporate a highly luminescent lanthanide beta-diketonate complex in a silica nanoparticle. Eu(btfa)3dmph complex was synthesized, which exhibits red luminescence at 614 nm with a narrow (15 nm) full with half-maximum (btfa=4,4,4-trifluoro-1-phenyl-1,3-butanedione, dmph=4,7-dimethyl,1,10-phenanthroline). A synthetic procedure was optimized to incorporate the Eu-complex in a silica-based nanoparticle with an average particle diameter of 36 nm. Eu-complex based silica nanoparticles exhibit high stability and water-dispersibility with a luminescence quantum yield of 10 %. The nanoparticles showed antimicrobial activity against clinically important E.coli, S.aureus and S.epidermidis. Synthesis, materials characterization, and antimicrobial studies of the complex and the nanoparticles was discussed in the first part of this thesis. Nanotechnology is emerging as a new interdisciplinary field combining biology, chemistry, physics, and material science. Recent advances promise developments in the synthesis, modification and practical applications of polymer-coated manganese (Mn)-based zinc oxide (ZnO) nanoparticles (NPs). The size distribution, shape, and surface modification of metal-based ZnO nanoparticles are the key factors determining their specific physical properties. Due to the strong antibacterial properties and low toxicity towards mammalian cells, ZnO NPs have been successfully used in a wide range of applications including wound dressing, protective clothing, antibacterial surfaces, food preservation, and cosmetics as biocidal and disinfecting agents. In this study, cotton textiles with antimicrobial activity were developed by incorporating polymer-coated Mn-doped ZnO nanoparticles. Antimicrobial potential of synthesized Mn-doped zinc oxide (ZnO) nanoparticles against two bacteria strains ( Escherichia coli as Gram-negative bacteria, Staphylococcus aureus as Gram-positive bacteria) in liquid and solid phases was studied in this work. Polymer-coated Mn-doped ZnO nanoparticles were prepared by the modified co-precipitation method. Characterization of the nanoparticles was carried out using Ultra-violet visible spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray powder diffraction (XRD). The average particle size of the nanoparticles was found to be less than 15 nm. The antibacterial activity of the nanoparticles was evaluated using minimum inhibitory concentration (MIC) and agar diffusion method. Disk diffusion studies revealed that the nanoparticles have excellent antimicrobial activity against E.coli and S.aureus bacterial species. Therefore, it was concluded that the polymer-coated Mn-doped ZnO nanoparticles were excellent antibacterial agents with potential clinical applications.

Let's Get Physical: Teaching Physics Through Gymnastics

NASA Astrophysics Data System (ADS)

Sojourner, Elena J.; Burgasser, Adam J.; Weise, Eric D.

2018-01-01

The concept of embodied learning—that we can learn with our bodies and with our minds—is a well-established concept in physics and math education research, and includes symbolic understanding (e.g., gestures that track how students think or facilitate learning to model complex systems of energy flow) as well as the literal experience of exploring physical phenomena through body movements. Sport has long served as a guide for both illustrating and experiencing physical concepts and phenomena, with a particularly relevant example being the sport of gymnastics. Here, the practitioner is subjected to a wide range of forces and torques, and experiences translational and rotational motions, all guided by control of body positioning, shape, strength, and leverage. Smith provides a comprehensive study of the mechanics used to analyze gymnastic movements, which includes core concepts such as force balance, leverage and torque, center of mass and stability, moment of inertia, ballistic motion, pendulum motion, and circular motion. For life science majors, gymnastics also provides relevant physical examples of biomechanics and the physical limits of biological materials (skin, bones, ligaments). The popularity of gymnastics—consider the phenomenon of Simone Biles—makes it broadly accessible and engaging, particularly across genders.

A Course in Biophysics: An Integration of Physics, Chemistry, and Biology

ERIC Educational Resources Information Center

Giancoli, Douglas C.

1971-01-01

Describes an interdisciplinary course for advanced undergraduates in the physical and biological sciences. The goal is to understand a living cell from the most basic standpoint possible. The ideas of physics, chemistry, and molecular biology are all essential to the course, which leads to a unified view of the sciences. (PR)

Biological physics in México: Review and new challenges.

PubMed

Hernández-Lemus, Enrique

2011-03-01

Biological and physical sciences possess a long-standing tradition of cooperativity as separate but related subfields of science. For some time, this cooperativity has been limited by their obvious differences in methods and views. Biological physics has recently experienced a kind of revival (or better a rebirth) due to the growth of molecular research on animate matter. New avenues for research have been opened for both theoretical and experimental physicists. Nevertheless, in order to better travel for such paths, the contemporary biological physicist should be armed with a set of specialized tools and methods but also with a new attitude toward multidisciplinarity. In this review article, we intend to somehow summarize what has been done in the past (in particular, as an example we will take a closer look at the Mexican case), to show some examples of fruitful investigations in the biological physics area and also to set a proposal of new curricula for physics students and professionals interested in applying their science to get a better understanding of the physical basis of biological function.

Anisotropic physical properties of myocardium characterized by ultrasonic measurements of backscatter, attenuation, and velocity

NASA Astrophysics Data System (ADS)

Baldwin, Steven L.

The goal of elucidating the physical mechanisms underlying the propagation of ultrasonic waves in anisotropic soft tissue such as myocardium has posed an interesting and largely unsolved problem in the field of physics for the past 30 years. In part because of the vast complexity of the system being studied, progress towards understanding and modeling the mechanisms that underlie observed acoustic parameters may first require the guidance of careful experiment. Knowledge of the causes of observed ultrasonic properties in soft tissue including attenuation, speed of sound, and backscatter, and how those properties are altered with specific pathophysiologies, may lead to new noninvasive approaches to the diagnosis of disease. The primary aim of this Dissertation is to contribute to an understanding of the physics that underlies the mechanisms responsible for the observed interaction of ultrasound with myocardium. To this end, through-transmission and backscatter measurements were performed by varying acoustic properties as a function of angle of insonification relative to the predominant myofiber direction and by altering the material properties of myocardium by increased protein cross-linking induced by chemical fixation as an extreme form of changes that may occur in certain pathologies such as diabetes. Techniques to estimate acoustic parameters from backscatter were broadened and challenges to implementing these techniques in vivo were addressed. Provided that specific challenges identified in this Dissertation can be overcome, techniques to estimate attenuation from ultrasonic backscatter show promise as a means to investigate the physical interaction of ultrasound with anisotropic biological media in vivo. This Dissertation represents a step towards understanding the physics of the interaction of ultrasonic waves with anisotropic biological media.

An Automated Peak Identification/Calibration Procedure for High-Dimensional Protein Measures From Mass Spectrometers.

PubMed

Yasui, Yutaka; McLerran, Dale; Adam, Bao-Ling; Winget, Marcy; Thornquist, Mark; Feng, Ziding

2003-01-01

Discovery of "signature" protein profiles that distinguish disease states (eg, malignant, benign, and normal) is a key step towards translating recent advancements in proteomic technologies into clinical utilities. Protein data generated from mass spectrometers are, however, large in size and have complex features due to complexities in both biological specimens and interfering biochemical/physical processes of the measurement procedure. Making sense out of such high-dimensional complex data is challenging and necessitates the use of a systematic data analytic strategy. We propose here a data processing strategy for two major issues in the analysis of such mass-spectrometry-generated proteomic data: (1) separation of protein "signals" from background "noise" in protein intensity measurements and (2) calibration of protein mass/charge measurements across samples. We illustrate the two issues and the utility of the proposed strategy using data from a prostate cancer biomarker discovery project as an example.

Integrating Mathematics into the Introductory Biology Laboratory Course

ERIC Educational Resources Information Center

White, James D.; Carpenter, Jenna P.

2008-01-01

Louisiana Tech University has an integrated science curriculum for its mathematics, chemistry, physics, computer science, biology-research track and secondary mathematics and science education majors. The curriculum focuses on the calculus sequence and introductory labs in biology, physics, and chemistry. In the introductory biology laboratory…

Evolution of an ancient protein function involved in organized multicellularity in animals

PubMed Central

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-01

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals. DOI: http://dx.doi.org/10.7554/eLife.10147.001 PMID:26740169

Perspective: Reaches of chemical physics in biology.

PubMed

Gruebele, Martin; Thirumalai, D

2013-09-28

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

Perspective: Reaches of chemical physics in biology

PubMed Central

Gruebele, Martin; Thirumalai, D.

2013-01-01

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry. PMID:24089712

Biological standards for the Knowledge-Based BioEconomy: What is at stake.

PubMed

de Lorenzo, Víctor; Schmidt, Markus

2018-01-25

The contribution of life sciences to the Knowledge-Based Bioeconomy (KBBE) asks for the transition of contemporary, gene-based biotechnology from being a trial-and-error endeavour to becoming an authentic branch of engineering. One requisite to this end is the need for standards to measure and represent accurately biological functions, along with languages for data description and exchange. However, the inherent complexity of biological systems and the lack of quantitative tradition in the field have largely curbed this enterprise. Fortunately, the onset of systems and synthetic biology has emphasized the need for standards not only to manage omics data, but also to increase reproducibility and provide the means of engineering living systems in earnest. Some domains of biotechnology can be easily standardized (e.g. physical composition of DNA sequences, tools for genome editing, languages to encode workflows), while others might be standardized with some dedicated research (e.g. biological metrology, operative systems for bio-programming cells) and finally others will require a considerable effort, e.g. defining the rules that allow functional composition of biological activities. Despite difficulties, these are worthy attempts, as the history of technology shows that those who set/adopt standards gain a competitive advantage over those who do not. Copyright © 2017 Elsevier B.V. All rights reserved.

Successful Aging: Advancing the Science of Physical Independence in Older Adults

PubMed Central

Anton, Stephen D.; Woods, Adam J.; Ashizawa, Tetso; Barb, Diana; Buford, Thomas W.; Carter, Christy S.; Clark, David J.; Cohen, Ronald A.; Corbett, Duane B.; Cruz-Almeida, Yenisel; Dotson, Vonetta; Ebner, Natalie; Efron, Philip A.; Fillingim, Roger B.; Foster, Thomas C.; Gundermann, David M.; Joseph, Anna-Maria; Karabetian, Christy; Leeuwenburgh, Christiaan; Manini, Todd M.; Marsiske, Michael; Mankowski, Robert T.; Mutchie, Heather L.; Perri, Michael G.; Ranka, Sanjay; Rashidi, Parisa; Sandesara, Bhanuprasad; Scarpace, Philip J.; Sibille, Kimberly T.; Solberg, Laurence M.; Someya, Shinichi; Uphold, Connie; Wohlgemuth, Stephanie; Wu, Samuel Shangwu; Pahor, Marco

2015-01-01

The concept of ‘Successful Aging’ has long intrigued the scientific community. Despite this long-standing interest, a consensus definition has proven to be a difficult task, due to the inherent challenge involved in defining such a complex, multi-dimensional phenomenon. The lack of a clear set of defining characteristics for the construct of successful aging has made comparison of findings across studies difficult and has limited advances in aging research. The domain in which consensus on markers of successful aging is furthest developed is the domain of physical functioning. For example, walking speed appears to be an excellent surrogate marker of overall health and predicts the maintenance of physical independence, a cornerstone of successful aging. The purpose of the present article is to provide an overview and discussion of specific health conditions, behavioral factors, and biological mechanisms that mark declining mobility and physical function and promising interventions to counter these effects. With life expectancy continuing to increase in the United States and developed countries throughout the world, there is an increasing public health focus on the maintenance of physical independence among all older adults. PMID:26462882

Using remote sensing to monitor past changes and assess future scenarios for the Sacramento-San Joaquin River Delta waterways, California USA

NASA Astrophysics Data System (ADS)

Santos, Maria J.; Hestir, Erin; Khanna, Shruti; Ustin, Susan L.

2017-04-01

Historically, deltas have been extensively affected both by natural processes and human intervention. Thus, understanding drivers, predicting impacts and optimizing solutions to delta problems requires a holistic approach spanning many sectors, disciplines and fields of expertise. Deltas are ideal model systems to understand the effects of the interaction between social and ecological domains, as they face unprecedented disturbances and threats to their biological and ecological sustainability. The challenge for deltas is to meet the goals of supporting biodiversity and ecosystem processes while also provisioning fresh water resources for human use. We provide an overview of the last 150 years of the Sacramento-San Joaquin River delta, where we illustrate the parallel process of an increase in disturbances, by particularly zooming in on the current cascading effects of invasive species on geophysical and biological processes. Using remote sensing data coupled with in situ measurements of water quality, turbidity, and species presence we show how the spread and persistence of aquatic invasive species affects sedimentation processes and ecosystem functioning. Our results show that the interactions between the biological and physical conditions in the Delta affect the trajectory of dominance by native and invasive aquatic plant species. Trends in growth and community characteristics associated with predicted impacts of climate change (sea level rise, warmer temperatures, changes in the hydrograph with high winter and low summer outflows) do not provide simple predictions. Individually, the impact of specific environmental changes on the biological components can be predicted, however it is the complex interactions of biological communities with the suite of physical changes that make predictions uncertain. Systematic monitoring is critical to provide the data needed to document and understand change of these delta systems, and to identify successful adaptation strategies.

Bioeffects of microwave--a brief review.

PubMed

Banik, S; Bandyopadhyay, S; Ganguly, S

2003-04-01

Since the 18th century scientists have been intrigued by the interaction of electromagnetic fields (EMFs) and various life processes. Attention has been focussed on EMFs in different frequency ranges, of which microwave frequency range forms an important part. Microwaves are part of the electromagnetic spectrum and are considered to be that radiation ranging in frequency from 300 million cycles per second (300 MHz) to 300 billion cycles per second (300 GHz), which correspond to a wavelength range of 1 m down to 1 mm. This nonionising electromagnetic radiation is absorbed at molecular level and manifests as changes in vibrational energy of the molecules or heat (Microwaves irradiating the community, Hidden hazards, Bantan Books publisher, Australia, 1991). Identifying and evaluating the biological effects of microwaves have been complex and controversial. Because of the paucity of information on the mechanism of interaction between microwave and biological systems, there has been a persistent view in physical and engineering sciences, that microwave fields are incapable of inducing bioeffects other than by heating (Health Physics 61 (1991) 3). Of late, the nonthermal effects of microwaves on tissue responses are being documented (Physiol. Rev. 61 (1981) 435; Annals of New York Acad. Sci. 247 (1975) 232; J. Microwave Power 14 (1979) 351; Bioelectromagnetics 7 (1986a) 45; Bioelectromagnetics 7 (1986b) 315; Biologic Effects and Health Hazards of Microwave Radiation, Warsaw, Polish Medical Publication (1974) 289; Biologic Effects and Health hazards of the microwave Radiation, Warsaw, Polish Medical Publication (1974) 22; Multidisciplinory perspectives in event-related brain potential research, Washington DC, US Environmental Protection Agency, (1978) 444). The present article is an attempt to familiarise the reader with pertinent information regarding the effects, mainly athermal, of microwave irradiation on biologic systems, especially microorganisms.

Toward University Modeling Instruction—Biology: Adapting Curricular Frameworks from Physics to Biology

PubMed Central

Manthey, Seth; Brewe, Eric

2013-01-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence. PMID:23737628

Toward university modeling instruction--biology: adapting curricular frameworks from physics to biology.

PubMed

Manthey, Seth; Brewe, Eric

2013-06-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence.

Getting the measure of things: the physical biology of stem cells.

PubMed

Lowell, Sally

2013-10-01

In July 2013, the diverse fields of biology, physics and mathematics converged to discuss 'The Physical Biology of Stem Cells', the subject of the third annual symposium of the Cambridge Stem Cell Institute, UK. Two clear themes resonated throughout the meeting: the new insights gained from advances in the acquisition and interpretation of quantitative data; and the importance of 'thinking outside the nucleus' to consider physical influences on cell fate.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Effects of Subject-Matter Knowledge in the Teaching of Biology and Physics.

ERIC Educational Resources Information Center

Hashweh, Maher Z.

An analysis of science teacher's knowledge of specific biology and physics topics and the effects of this knowledge on their planning for instruction and on simulated teaching are discussed in this report. Six experienced secondary school teachers participated in the study. Each teacher's knowledge of a biology topic and a physics topic was…