Models of biological systems and biological processes

1994 ◽  
Vol 66 (4) ◽  
pp. 759-764 ◽  
Author(s):  
U. K. Pandit
Keyword(s):  
Biological Systems ◽  
Biological Processes

Integrating the whole from the sum of the parts: vignettes in computational biology

2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Personalized Medicine ◽  
Computational Biology ◽  
Biological Systems ◽  
Deep Understanding ◽  
Biological Processes ◽  
Practical Applications ◽  
Biological Variables

As is typical of contemporary cutting-edge interdisciplinary fields, computational biology touches and impacts many disciplines ranging from fundamental studies in the areas of genomics, proteomics transcriptomics, lipidomics to practical applications such as personalized medicine, drug discovery, and synthetic biology. This editorial examines the multifaceted role computational biology plays. Using the tools of deep learning, it can make powerful predictions of many biological variables, which may not provide a deep understanding of what factors contribute to the phenomena. Alternatively, it can provide the how and the why of biological processes. Most importantly, it can help guide and interpret what experiments and biological systems to study.

Van der Waals forces in biological systems

1973 ◽  
Vol 6 (4) ◽  
pp. 341-387 ◽  
Author(s):  
Jacob N. Israelachvili
Keyword(s):  
Biological Systems ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
Biological Processes ◽  
Theoretical Investigations ◽  
The Way

The theory of van der Waals forces has now developed to a stage where it constitutes a powerful tool in theoretical investigations of many biological systems. In this review we shall consider both the theoretical and conceptual aspects of these forces with the emphasis on the way they may be involved in various biological processes.

scholarly journals Cross-species comparisons and in vitro models to study tempo in development and homeostasis

2021 ◽  
Vol 11 (3) ◽  
Author(s):  
Teresa Rayon ◽  
James Briscoe
Keyword(s):  
Biological Systems ◽  
In Vitro Models ◽  
Autonomous Control ◽  
Tissue Transplantation ◽  
Biological Processes ◽  
Open Questions ◽  
Species Comparisons ◽  
Insight Into

Time is inherent to biological processes. It determines the order of events and the speed at which they take place. However, we still need to refine approaches to measure the course of time in biological systems and understand what controls the pace of development. Here, we argue that the comparison of biological processes across species provides molecular insight into the timekeeping mechanisms in biology. We discuss recent findings and the open questions in the field and highlight the use of in vitro systems as tools to investigate cell-autonomous control as well as the coordination of temporal mechanisms within tissues. Further, we discuss the relevance of studying tempo for tissue transplantation, homeostasis and lifespan.

Numerical Simulation of a Physiological Mathematical Model of Energy Consumption in a Sarcomere

2021 ◽  
Author(s):  
◽  
K. G. Flores-Rodríguez
Keyword(s):  
Calcium Release ◽  
Biological Systems ◽  
Muscular Contraction ◽  
Muscle Group ◽  
Point Of View ◽  
Estimation Methods ◽  
Biological Processes ◽  
Group Level ◽  
Force Velocity ◽  
Analytical Tools

The paradigm of biological systems provides a framework to quantify the behavior of biological processes. Mathe-matical modeling is one of the analytical tools of biological systems used to reproduce the variables of a system for prediction. This article presents the analysis of muscular contraction, the physiological process responsible of generating force in skeletal muscle, from the point of view of mathematical modeling. The aim is to provide nume-rical evidences about the force generated by the sarcomere, and the energy required to produce such a force. The proposed scheme includes a model to activate the contractile cycle, based on the action potential that reaches the neuromuscular junction, the calcium release into the sarcoplasm, the contraction response, and the quantification of the energy that the sarcomere requires to perform mechanical work. The results shows that the proposed scheme is acceptable because it reproduces experimental data of force, velocity, and energy reported in the literature. The results of the proposed scheme are encouraging to scale the model at the muscle or muscle group level, in such a way that the quantification of energy can be an alternative to the indirect estimation methods of energy consump-tion that currently exist.

scholarly journals Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Biosensors ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 100 ◽  
Author(s):  
Marta Neves ◽  
Daniel Martín-Yerga
Keyword(s):  
Nucleic Acids ◽  
Physicochemical Properties ◽  
Biological Systems ◽  
Life Sciences ◽  
Biological Processes ◽  
Average Response ◽  
Single Entity ◽  
Conventional Methods ◽  
Stochastic Events ◽  
Conventional Detection

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.

scholarly journals Stochastic reaction networks in dynamic compartment populations

2020 ◽  
Vol 117 (37) ◽  
pp. 22674-22683
Author(s):  
Lorenzo Duso ◽  
Christoph Zechner
Keyword(s):  
Biological Systems ◽  
Reaction Dynamics ◽  
Theoretical Models ◽  
Counting Processes ◽  
Mathematical Framework ◽  
Biological Processes ◽  
Biochemical Processes ◽  
Subcellular Compartmentalization ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks

Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and typically very challenging to analyze computationally. Recent studies have made progress toward addressing this problem in the context of specific biological systems, but a general and sufficiently effective approach remains lacking. In this work, we propose a mathematical framework based on counting processes that allows us to study dynamic compartment populations with arbitrary interactions and internal biochemistry. We derive an efficient description of the dynamics in terms of differential equations which capture the statistics of the population. We demonstrate the relevance of our approach by analyzing models inspired by different biological processes, including subcellular compartmentalization and tissue homeostasis.

Applications of ultrafast laser spectroscopy for the study of biological systems

1989 ◽  
Vol 22 (3) ◽  
pp. 239-326 ◽  
Author(s):  
Alfred R. Holzwarth
Keyword(s):  
Molecular Level ◽  
Biological Systems ◽  
Ultrashort Pulses ◽  
Chemical Processes ◽  
Ultrafast Laser ◽  
Relaxation Processes ◽  
Biological Processes ◽  
Ultrafast Laser Spectroscopy ◽  
Physical And Chemical ◽  
First Time

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.

Sign in / Sign up

Export Citation Format

Share Document