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The cell conservation equation has the form ${\bar{n}}_{\bar{t}}=-\bar{\nabla }\cdot \bar{\mathbf{J}}$, withThe first term is advection by the suspension's fluid velocity, the second is active swimming at fixed speed $V_c$ in direction $\mathbf{p}$, and the last is an isotropic diffusive flux due to random swimming. Here $D$ has units length squared per time, $\bar{n}$ is cell number per volume, and the divergence measures local loss by transport. No birth or death term is included.

For a spherical cell of radius $a_c$, its excess buoyancy force is $(4\pi a_c^3/3)\Delta \rho g$. The Stokes drag law gives passive settling speed $V_{\mathrm{set}}=2a_c^2\Delta \rho g/(9\mu )$. Neglecting individual settling requires $V_{\mathrm{set}}\ll V_c$, not exact neutral buoyancy. A dilute suspension can still generate appreciable collective buoyancy because many small excess masses contribute to the bulk density.

Use the half-rate convention for the gyrotactic reorientation time $B$, required by the coefficients printed in the question:The first torque tends to point the bottom-heavy cell upward; the second rotates a sphere with half the fluid vorticity. This is a quasistatic torque balance, assuming orientation relaxation is fast enough to follow the local flow. Keeping orientation dynamics instead would put $d\mathbf{p}/d\bar{t}$ on the left. The convention with aligning rate $1/B$ uses a reorientation parameter twice this $B$. Thus the factor of two is a definition, not a physical discrepancy. Close to the upward state the quasistatic gyrotactic balance with half-rate reorientation gives ${\mathbf{p}}_{\perp }=B\bar{\mathbf{\omega }}\times {\mathbf{e}}_z$.

For a dilute Newtonian suspension with the Boussinesq approximation, the other equations areThe background-water hydrostatic pressure is absorbed in $\bar{p}$. The cell volume is $\upsilon$, density is $\rho$, cell density is $\rho +\Delta \rho$, dynamic viscosity is $\mu =\rho \nu$, and $\upsilon \bar{n}\ll 1$ is the volume fraction. Extra cell mass produces the downward buoyancy term. Constant viscosity and no explicit swimming stress are part of this closure. Rigid impermeable plates impose no-slip boundary condition and zero normal total cell flux.

At rest, the stable cell direction is upward and the steady vertical flux is $V_c\bar{n}-D{\bar{n}}_{\bar{z}}$. It is constant in depth by conservation and zero at an impermeable plate, soThe pressure gradient balances its excess weight. The mean-concentration formula follows by averaging over $0\le \bar{z}\le h$ and is continuous at $\beta =0$.

Use $\mathbf{x}=\bar{\mathbf{x}}/h$, $t=D\bar{t}/h^2$, $\mathbf{u}=h\bar{\mathbf{u}}/D$, $n=\bar{n}/{\bar{N}}_0$, and $p=h^2\bar{p}/(\rho \nu D)$. ThenwhereThe dimensionless base concentration is $n_0=e^{\beta z}$.

Linearize with the horizontal Fourier mode $e^{\sigma t+ilx+imy}$ and $k^2=l^2+m^2$. Write the first-order orientation perturbation as $\mathbf{p}={\mathbf{e}}_z+ϵ{\mathbf{p}}_1+\cdots$. Unit length gives $p_{1z}=0$, while torque balance gives ${\mathbf{p}}_{1\perp }=G{\mathbf{\omega }}_1\times {\mathbf{e}}_z$. Incompressibility impliesLet $\mathcal{L}=d^2/d{z}^2-k^2$. The perturbation of fluid advection is $n_0^{\prime }W=\beta n_{0}W$, and swimming contributes $\beta N^{\prime }+\beta n_0\nabla \cdot {\mathbf{p}}_1$. Cell conservation therefore givesorThis explains the destabilizing concentration-advection term and the gyrotactic redistribution term with their signs.

To eliminate pressure from the fluid equations, take their divergence, giving $\mathcal{L}{p}_1=-(R/\beta )N^{\prime }$. Apply $\mathcal{L}$ to the vertical equation $S{c}^{-1}\sigma W=-p_1^{\prime }+\mathcal{L}W-(R/\beta )N$. The concentration second derivatives cancel, leavingNo-slip conditions give $W=0$ and $W^{\prime }=0$ at each plate; for nonzero $k$, the latter follows from the vanishing horizontal velocity and incompressibility. Zero perturbed normal cell flux givesThe normal orientation correction is zero at this order, and the fluid velocity is zero at the plate, so neither adds another term to this concentration condition.

Now use the stated distinguished scalings $k=\beta \alpha$, $\sigma ={\beta }^2{\sigma }_2$, $G={\beta }^{-1}{G}_{-1}$, $N=N_0+\beta N_1+{\beta }^2{N}_2+\cdots$, $W=\beta W_1+{\beta }^2{W}_2+\cdots$, and $R=R_0+\beta R_1+\cdots$. Here $\alpha$ is a scaled wavenumber, unrelated to Question 2's shear rate. At order one, the concentration equation and boundary conditions give $N_0^{\prime \prime }=0$, $N_0^{\prime }=0$ at both endpoints, so $N_0$ is constant. Absorb its nonzero value into the perturbation amplitude and chooseAt order $\beta$, the fluid equation is $W_1^{(4)}=-R_0{\alpha }^2$ with $W_1=W_1^{\prime }=0$ at both ends. Its unique solution isA homogeneous difference is cubic and the four clamped conditions make it zero.

The concentration equation at order $\beta$ givesso $N_1=z-G_{-1}{W}_1+C_1$, where $C_1$ fixes the amplitude normalization. At order ${\beta }^2$ it givesThe boundary conditions expand to $N_2^{\prime }=N_1$ at each endpoint. Integrating this equation from zero to one cancels $[N_2^{\prime }{]}_0^1$ against $[N_1{]}_0^1$. Also $[W_2^{\prime }{]}_0^1=0$ andThus the required solvability condition isSince ${\int }_0^1{z}^2(1-z{)}^{2}dz=1/30$, the clamped-quartic solvability in shallow bioconvection gives

For nonzero long horizontal waves, $R_0<720$ gives decay and $R_0>720$ gives growth; the leading neutral threshold is $R_0=720$. The leading instability is stationary and independent of $G_{-1}$ and $Sc$. The exactly uniform horizontal mode $\alpha =0$ has zero growth at this order because total cell number is conserved, so it does not determine the threshold. Upward swimming produces a dense upper layer; the unstable disturbance is its buoyancy-driven overturning, or bioconvection. Higher orders are needed for wavelength selection and finite-depth threshold corrections.

With fixed material parameters and mean concentration, $R\sim h^4{V}_c\upsilon \Delta \rho g{\bar{N}}_{00}/(\rho \nu D^2)$ for small $\beta$, so a sufficiently thin chamber is stable to this branch. Formally its threshold corresponds to $h_c\sim [720\rho \nu D^2/(V_c\upsilon \Delta \rho g{\bar{N}}_{00}){]}^{1/4}$ when the weak-stratification and distinguished-gyrotaxis assumptions apply. In particular, the assumed $G=O({\beta }^{-1})$ is a specified asymptotic analysis; at fixed $B,D,V_c$ and decreasing $h$, one instead has $G=O({\beta }^{-2})$. The leading result should not be asserted unchanged in that different ordering without redoing the expansion.

Fix the sense of rotation by taking the fluid velocity to be $\mathbf{u}=\Omega (-x_3,0,x_1)$, with $\Omega >0$. Its vorticity is $-2\Omega {\mathbf{e}}_2$. In the convention where $B$ is the gyrotactic reorientation time appearing with aligning rate $1/B$, the bottom-heavy spherical-cell orientation dynamics isFor the stable orientation in the transverse plane, write $\mathbf{p}=(\sin \vartheta ,0,\cos \vartheta )$. The angle equation is $\dot{\vartheta }=-\sin \vartheta /B-\Omega$. If $B\Omega <1$, its stable fixed point satisfiesThe other planar fixed point has negative $p_3$ and is unstable. The positive-$p_3$ orientation also damps a small out-of-plane component because ${\dot{p}}_2=-p_3{p}_2/B$.

Once the orientation has relaxed to ${\mathbf{p}}_{\ast }$, the transverse trajectory obeysDefine the shifted axis byThen $(x_1-x_{1A},x_3-x_{3A})$ rotates rigidly with angular speed $\Omega$, so its squared length is constant. These are the gyrotactic circular paths in a rotating cylinder, andHere $\alpha$ is the acute angle between the plane through the two parallel axes and the horizontal plane; the directed displacement $OA$ in the chosen cross-section points to the lower-left. Reversing the sense of rotation reverses the horizontal displacement. Arbitrary initial orientations have an orientation transient before the exact circular trajectories; neglecting randomness alone does not remove that transient. The bulk result also assumes that the trajectory does not intersect the cylinder wall.

Write ${\ell }_g$ for the dimensional offset of the centre of mass, reserving $h$ below for the dimensionless swimming parameter. The weight $-mg\mathbf{k}$ acts at $-{\ell }_g\mathbf{p}$, so its torque about the geometric centre is $mg{\ell }_g\mathbf{p}\times \mathbf{k}$. Buoyancy acts through the geometric centre and has no such torque. For a spherical cell, the ambient angular velocity is $\mathbf{\omega }/2$ and the rotational resistance is ${\zeta }_r=\rho \nu {\alpha }_{\perp }v$. Neglecting angular inertia, torque balance givesSince $\dot{\mathbf{p}}={\mathbf{\Omega }}_{\mathrm{cell}}\times \mathbf{p}$, the bottom-heavy spherical-cell orientation dynamics isThus a steady orientation satisfiesThe printed algebraic equation has the opposite sign on its right side, if vorticity means the usual $\nabla \times \mathbf{u}$. Its later concentration equation is consistent with the corrected sign. In particular, linearizing the corrected equation about $\mathbf{p}=\mathbf{k}$ gives ${\mathbf{p}}_{\perp }=(B/2)(\mathbf{\omega }\times \mathbf{k}{)}_{\perp }$, whereas the printed sign would reverse that response. Merely changing the definition of vorticity would also require changing the ensuing fluid and orientation calculations.

The gyrotactic reorientation time $B$ measures gravitational restoration against rotational viscous resistance. In still fluid a tilt angle obeys $\dot{\theta }=-\sin \theta /B$, soFor small tilt it is precisely the exponential relaxation time. Applying the algebraic orientation balance to a time-dependent disturbance additionally assumes that this relaxation is fast enough to neglect orientation lag. Keeping the full dynamic orientation equation would introduce an additional relaxation factor into the perturbation problem.

This convention defines the gyrotactic reorientation time by an aligning rate $1/(2B)$. Multiplying the torque balance by $2B$ and perturbing about the upward direction gives ${\mathbf{p}}_{\perp }=B\mathbf{\omega }\times {\mathbf{e}}_z$. For an incompressible flow, its horizontal divergence is $-B{\nabla }^{2}w$, because $\nabla \times \mathbf{\omega }=-{\nabla }^2\mathbf{u}$. The parameter $B$ is half the reorientation parameter used in the convention with aligning rate $1/B$; writing the governing equation prevents a factor-of-two ambiguity.