In cell biology, the cytoplasm describes all material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol, the organelles, and various cytoplasmic inclusions. The cytoplasm is about 80% water and is usually colorless.
Facilitated diffusion is the process of spontaneous passive transport of molecules or ions across a biological membrane via specific transmembrane integral proteins. Being passive, facilitated transport does not directly require chemical energy from ATP hydrolysis in the transport step itself; rather, molecules and ions move down their concentration gradient reflecting its diffusive nature.
The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and membranes of the membrane-bound organelles in the cell. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps.
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
The fluid mosaic model explains various observations regarding the structure of functional cell membranes. According to this biological model, there is a lipid bilayer in which protein molecules are embedded. The phospholipid bilayer gives fluidity and elasticity to the membrane. Small amounts of carbohydrates are also found in the cell membrane. The biological model, which was devised by Seymour Jonathan Singer and Garth L. Nicolson in 1972, describes the cell membrane as a two-dimensional liquid that restricts the lateral diffusion of membrane components. Such domains are defined by the existence of regions within the membrane with special lipid and protein cocoon that promote the formation of lipid rafts or protein and glycoprotein complexes. In addition, it came before the other model that introduced the first bilayer. Another way to define membrane domains is the association of the lipid membrane with the cytoskeleton filaments and the extracellular matrix through membrane proteins. The current model describes important features relevant to many cellular processes, including: cell-cell signaling, apoptosis, cell division, membrane budding, and cell fusion. The fluid mosaic model is the most acceptable model of the plasma membrane. Its main function is to separate the contents of the cell from the exterior.
Fluorescence recovery after photobleaching (FRAP) is a method for determining the kinetics of diffusion through tissue or cells. It is capable of quantifying the two-dimensional lateral diffusion of a molecularly thin film containing fluorescently labeled probes, or to examine single cells. This technique is very useful in biological studies of cell membrane diffusion and protein binding. In addition, surface deposition of a fluorescing phospholipid bilayer allows the characterization of hydrophilic surfaces in terms of surface structure and free energy.
The plasma membranes of cells contain combinations of glycosphingolipids, cholesterol and protein receptors organised in glycolipoprotein lipid microdomains termed lipid rafts. Their existence in cellular membranes remains somewhat controversial. It has been proposed that they are specialized membrane microdomains which compartmentalize cellular processes by serving as organising centers for the assembly of signaling molecules, allowing a closer interaction of protein receptors and their effectors to promote kinetically favorable interactions necessary for the signal transduction. Lipid rafts influence membrane fluidity and membrane protein trafficking, thereby regulating neurotransmission and receptor trafficking. Lipid rafts are more ordered and tightly packed than the surrounding bilayer, but float freely within the membrane bilayer. Although more common in the cell membrane, lipid rafts have also been reported in other parts of the cell, such as the Golgi apparatus and lysosomes.
Fluorescence correlation spectroscopy (FCS) is a statistical analysis, via time correlation, of stationary fluctuations of the fluorescence intensity. Its theoretical underpinning originated from L. Onsager's regression hypothesis. The analysis provides kinetic parameters of the physical processes underlying the fluctuations. One of the interesting applications of this is an analysis of the concentration fluctuations of fluorescent particles (molecules) in solution. In this application, the fluorescence emitted from a very tiny space in solution containing a small number of fluorescent particles (molecules) is observed. The fluorescence intensity is fluctuating due to Brownian motion of the particles. In other words, the number of the particles in the sub-space defined by the optical system is randomly changing around the average number. The analysis gives the average number of fluorescent particles and average diffusion time, when the particle is passing through the space. Eventually, both the concentration and size of the particle (molecule) are determined. Both parameters are important in biochemical research, biophysics, and chemistry.
A single-molecule experiment is an experiment that investigates the properties of individual molecules. Single-molecule studies may be contrasted with measurements on an ensemble or bulk collection of molecules, where the individual behavior of molecules cannot be distinguished, and only average characteristics can be measured. Since many measurement techniques in biology, chemistry, and physics are not sensitive enough to observe single molecules, single-molecule fluorescence techniques caused a lot of excitement, since these supplied many new details on the measured processes that were not accessible in the past. Indeed, since the 1990s, many techniques for probing individual molecules have been developed.
Anomalous diffusion is a diffusion process with a non-linear relationship between the mean squared displacement (MSD), , and time. This behavior is in stark contrast to Brownian motion, the typical diffusion process described by Einstein and Smoluchowski, where the MSD is linear in time. Examples of anomalous diffusion in nature have been observed in biology in the cell nucleus, plasma membrane and cytoplasm.
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches.
In biology, membrane fluidity refers to the viscosity of the lipid bilayer of a cell membrane or a synthetic lipid membrane. Lipid packing can influence the fluidity of the membrane. Viscosity of the membrane can affect the rotation and diffusion of proteins and other bio-molecules within the membrane, there-by affecting the functions of these things.
In membrane biology, fusion is the process by which two initially distinct lipid bilayers merge their hydrophobic cores, resulting in one interconnected structure. If this fusion proceeds completely through both leaflets of both bilayers, an aqueous bridge is formed and the internal contents of the two structures can mix. Alternatively, if only one leaflet from each bilayer is involved in the fusion process, the bilayers are said to be hemifused. In hemifusion, the lipid constituents of the outer leaflet of the two bilayers can mix, but the inner leaflets remain distinct. The aqueous contents enclosed by each bilayer also remain separated.
In biophysics and related fields, reduced dimension forms (RDFs) are unique on-off mechanisms for random walks that generate two-state trajectories (see Fig. 1 for an example of a RDF and Fig. 2 for an example of a two-state trajectory). It has been shown that RDFs solve two-state trajectories, since only one RDF can be constructed from the data, where this property does not hold for on-off kinetic schemes, where many kinetic schemes can be constructed from a particular two-state trajectory (even from an ideal on-off trajectory). Two-state time trajectories are very common in measurements in chemistry, physics, and the biophysics of individual molecules (e.g. measurements of protein dynamics and DNA and RNA dynamics, activity of ion channels, enzyme activity, quantum dots ), thus making RDFs an important tool in the analysis of data in these fields.
A two-state trajectory is a dynamical signal that fluctuates between two distinct values: ON and OFF, open and closed, , etc. Mathematically, the signal has, for every either the value or .
The fences and pickets model of plasma membrane is a concept of cell membrane structure suggesting that the fluid plasma membrane is compartmentalized by actin-based membrane-skeleton “fences” and anchored transmembrane protein “pickets”. This model differs from older cell membrane structure concepts such as the Singer-Nicolson fluid mosaic model and the Saffman-Delbrück two-dimensional continuum fluid model that view the membrane as more or less homogeneous. The fences and pickets model was proposed to explain observations of molecular traffic made due to recent advances in single molecule tracking techniques.
Interferometric scattering microscopy (iSCAT) refers to a class of methods that detect and image a subwavelength object by interfering the light scattered by it with a reference light field. The underlying physics is shared by other conventional interferometric methods such as phase contrast or differential interference contrast, or reflection interference microscopy. The key feature of iSCAT is the detection of elastic scattering from subwavelength particles, also known as Rayleigh scattering, in addition to reflected or transmission signals from supra-wavelength objects. Typically, the challenge is the detection of tiny signals on top of large and complex, speckle-like backgrounds. iSCAT has been used to investigate nanoparticles such as viruses, proteins, lipid vesicles, DNA, exosomes, metal nanoparticles, semiconductor quantum dots, charge carriers and single organic molecules without the need for a fluorescent label.
Rae Marie Robertson-Anderson is an American biophysicist who is Associate Professor at the University of San Diego. She works on soft matter physics and is particularly interested in the transport and molecular mechanics of biopolymer networks. Robertson-Anderson is a member of the Council on Undergraduate Research.
Suliana Manley is an American biophysicist. Her research focuses on the development of high-resolution optical instruments, and their application in studying the organization and dynamics of proteins. She is a professor at École Polytechnique Fédérale de Lausanne and heads the Laboratory of Experimental Biophysics.
Diego Krapf is an Argentine-Israeli-American physicist known for his work on anomalous diffusion and ergodicity breaking. He currently is a professor in the Department of Electrical and Computer Engineering at Colorado State University.
