Questions tagged [biophysics]

The use of methods from the physical sciences to aid in the study of biological systems.

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24 views

Can lead field be a scalar field? [closed]

In electrophysiology it is common to use lead (vector) field to describe relation between electric activity described as an electric dipole and the potential measured at electrodes. Can the term "...
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34 views

How do signalling molecules find their receptors at large distances?

I have been baffled with this question approx. for a dozen of years for now. There is a default "lock & key" mechanism of action assumed for the interaction between a signalling molecule and its ...
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51 views

How does energy conversion happen (chemical to mechanical?) in moving body muscles?

From my understanding, the brain sends electrical pulses through neurons to different part of the body to initiate a movement. My question is, how is the movement realized? For example, in a train, ...
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20 views

How to include multiple DNAs into a crystal structure

I have a crystal structure (PDB 3OS1)that shows the interaction of PFV intasome with a substate DNA. I would like to replace the existing DNA in the intasome as well in the substrate with a longer ...
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45 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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43 views

Which proteins are most sensitive to electric fields?

Many Proteins have ionic charges that can attract each other (e.g. Formation of salt bridges) or repel each other. On the other Hand, Proteins are mostly immersed in water that screens most of the ...
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Does the Rayleigh formula apply to electron microscopes or only light microscopes?

I am asked to determine the resolving power of both a TEM (transmission electron microscope) and a SEM (scanning electron microscope) and given the Rayleigh formula below. $$Resolution=\frac{0.61\...
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50 views

Bioenergetics book

I already asked this question on the physics SE but redirected here: In the field of biophysics, it seems there is a subfield called "bioenergetics" about the processes of generating energy by ...
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Can UV radiation be safe for the skin?

It is well known that UV radiation can damage the DNA and generally harm our skin. We also know that UV radiation helps on the production of melanin and Vitamin D. From what I could find, the DNA ...
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“Straight” or “linear” helix

If an alpha helix is discontinued for a short while and then continues in a different direction, I prefer to call in "kinked". If the helix is simply uniformly following one direction, I prefer to ...
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What is the native structure of amyloid-beta protein under physiological conditions?

The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?
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Why is wound contraction very slow?

I am working on mathematical model for healing of dermal wounds. For anyone who's a bit familiar with Physics and Math, for the model I use the Cauchy Momentum Equation as a basis, and from there I ...
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What are the methods to measure the surface density of animals in biology?

In biology there is a rule found by Damuth (https://www.nature.com/articles/290699a0): a relationship between the size of an animal species $l$ and its local abundance (surface density) $N/S$ $$N/S=...
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104 views

Where does this equation in the electrophysiology literature form come from?

In my studies I keep coming across the form of an equation that is used in many different mathematical models for voltage gated ion channels. The most general form I have found is in the 1977 paper ...
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31 views

How many frames per second do human eyes see? [duplicate]

I observed when a helicopter rotor or fan is spinning the blades blur making it impossible to count the blades, but after a certain speed the blades seem to become visible making it possible to count ...
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How does nitrogen gas partial pressure change when ascending during scuba dive?

Scuba divers suffer decompression illness in which during sudden ascension, gas bubbles form in blood vessels and do not get reabsorbed quickly, leading to various problems including a stroke. The ...
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Time span until everything biological is stabilized/finalized after a low-level exposure to ionizing radiation?

Say the x-rays of a common diagnostic CT (< = 10 mSv?). Irrespective of any ultimate effects (linear or threshold detrimental, inconsequential, or even protectively hormetic) just how long until ...
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38 views

Entropy during neuronal signaling

to begin with: I have some background in cognitive neuroscience, but have not intensely studied the biochemical background of neuronal signalling, so please correct me if my basic understanding is ...
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94 views

Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
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347 views

Difference between prions and amyloid proteins?

Amyloid and prions are misfolded proteins, but what, if any, is the difference between them? Is amyloid a type of prion with a fibrillar structure?
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How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression $$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ ...
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199 views

Why is there a layer of moist lining the inner walls of alveoli?

I'm taught that the walls of the alveoli are moist, so gaseous oxygen molecules can dissolve into this water. This then allows the dissolved oxygen (liquid state) to diffuse faster from the alveoli ...
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32 views

Why does the DSC peak have a bell shape?

I am studying Differential Scanning Calorimetry (DSC) and am not quite understanding why most proteins have a bell shape when the heat capacity is plotted against the temperature. Also, I would ...
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94 views

Why biologic systems tends to become more complex?

From elements, chemical compounds, cells, multicellular organisms, society evolves and with each step possibilities increase and things get complex. We are builing structures like ribosome builds ...
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Effects of horizontal vs. vertical motion on human body

I want to know if moving along a vertical plane in a circle differs in its effects on the human body from moving horizontally in a circle. Imagine a ferris wheel with a diameter of 50 metres. If a ...
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267 views

Why do neurons have long axons but short dendrites?

Cian O'Donnell, a British neuroscientist, originally asked this question on Twitter: https://twitter.com/cian_neuro/status/1075432086692089857. I am not a biophysicist by training but I wonder whether ...
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142 views

Can light function as a neurotransmitter?

Any animal with an eye has photoreceptors, which are essentially light-sensitive neurons. Green algae have channelrhodopsin, which are ion channels that open and close in response to light. Clearly, ...
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156 views

What is meant with “the chest wall and lungs are coupled together”?

Since the lung and chest are elastic, we can represent them with springs. Under normal conditions, they are coupled together: the “lung” springs are stretched and the “chest” springs are compressed. ...
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70 views

How are sound waves amplified while traveling within the cochlea?

How are sound waves amplified while traveling from the basal membrane to apical membrane within the cochlea? Are they amplified by the movement of the stapes?
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35 views

What is (are) the medium of conduction for an electrical current with an external source in the human body?

I am trying to get some background for some personal research I am doing into the effects of Electro Convulsive Therapy. I don't understand how electric current from an external household source, say, ...
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78 views

What waste products do cells secrete in culture, and at what rate?

I am designing microfluidic chips for mammalian cell culture. One aspect I am interested in modeling is the rate at which I must renew media to ensure that: Cells receive enough nutrients Cytotoxic ...
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1answer
500 views

Can multiple antibodies bind the same antigen?

Given the size difference between small molecule antigens and antibodies is it ever possible for multiple antibodies to bind to the same antigen if they recognize different domains on that antigen? ...
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29 views

Square-cubed law and health

Does the square-cubed law lead to possible health detriments for taller people? I'm not sure what the optimum height is for humans (e.g. due to their cross-sectional bone density constraints), but ...
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26 views

Is it possible to induce protein activation via frequency-specific mechanical waves? [closed]

Would it be possible to induce shape changes in specific proteins by providing specific frequencies of mechanical waves in a thermostatically controlled environment such that those proteins may be ...
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71 views

How can diving with 100% oxygen not destroy your lungs? [closed]

It is possible this should be moved to physics, depending on the nature of the answer (i.e. if the reason is physical). But I suspect the explanation is biological, so I posted it here. Sometimes ...
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76 views

Fraction of channels open at equilibrium

I found the formula for the fraction of channels open at equilibrium for a three-state mechanism (Colquhoun's paper in the microelectrode book http://www.utdallas.edu/~tres/microelectrode/me.html) k1 ...
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109 views

Are resonances the reason receptors work?

From Visual phototransduction - Wikipedia: When struck by a photon, 11-cis retinal undergoes photoisomerization to all-trans retinal which changes the conformation of the opsin GPCR leading to ...
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42 views

Is summation linear in a passive membrane?

I am not too sure what it means for summation to be linear? I am running a simulation and as I decrease time for the second EPSP the amplitude decreases. Does summation being linear mean that there is ...
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806 views

Why does UVA penetrate deeper than UVB, though it's weaker?

Even though UVA radiation ranges in longer wavelengths (315–400 nm) than UVB (280–315 nm) and thus is less energetic, UVA is able to penetrate deeper into the skin and even reach the dermis. Why is ...
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50 views

effect of arterial vasocontriction on the pressure in arteries

if experimentally one induces smooth muscle contraction on an artery and cause it to constrict, keeping the cardiac output same and also the arteriolar resistance(total peripheral resistance) the same ...
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135 views

What is the biological relevance of RIPPLE phase in membranes?

I was reading about ripple phase in bilayer lipid membranes which is described here as a meta-stable state between lamellar tilted crystalline and lamellar fluid state. It is also known that ripple ...
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Causes of the stochastic behaviour of voltage-gated ion channels

I came up with the following electro-mechanical model of a voltage-gated ion channel, resp. of its voltage sensor as described here and here. The voltage sensor is a bistable system with two local ...
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law of laplace and pressure developed in arteries

in arterioles the pressure depends on the impedance of the vessel(elasticity and youngs modulus) cardiac output pre arteriolar resistance what i want to ask is will the pressure also depend on law of ...
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36 views

Calcium and nitric oxide: does a numerical relationship exist?

Currently, I am trying to understand how nitric oxide and calcium are related during the production of the former (I am not a biologist nor a chemist, so my knowledge about these topics is very poor). ...
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546 views

How can some residues in the active site of enzymes be protonated with a pKa < 7?

It is reported in many papers, that some residues in the active site of enzymes need to be protonated to get functional enzyme, where these residues have a low pKa (for let us say 5). How can that ...
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Validity of Acoustic Weapon Effects on Biological Organisms?

There is alot of rather contradictory information present on the biological effects of acoustic weapons with a bevy of scientific articles claiming that they cause harm to biological organisms with ...
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144 views

What is the point in the Neuromuscular Junction?

Surely a direct connection (i.e. an electrical synapse) between motor neurone and the sarcolemma would allow for much faster neuromuscular transmission? It is my understanding that chemical synapses ...
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Are trees still carrying their leaves more likely to be felled by an autumn storm?

Is there evidence that trees still carrying their leaves are more likely to be felled by an autumn storm than trees already having lost their leaves? At first sight this seems plausible (and might be ...
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342 views

How interrelated are computational biology and biophysics? [closed]

I am considering applying to Ph.D. programs, and am not sure what direction to take. I'm hoping you all can help me out. I have a background in both biology (molecular focus) and physics (condensed ...
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Calcium concentration in activated dendritic spines?

What are the typical calcium levels reached in single postsynaptic spines following activation of NMDA receptors by an EPSP or backpropagating spike? Everyone seems to refer to that one Neuron paper (...